[e-mail]

1
???????????????????
????????????
2008?5?13?(?)

• ???????????????????
• ?? ?
• takawaba_at_is.naist.jp

http//isw3.naist.jp/IS/Kawabata-lab/home-ja.html
2
????
?? ?? ?? ??
4/8(?) ?? ??????????????
4/15(?) ?? ????1 IMC?????????
4/22(?) ?? ????2 IMC???????????
5/13(?) ?? ???????????????????
5/20(?) ?? ??????????????????? ???????????????
5/27(?) ?? ???????????????
6/3(?) ?? ????????????????? ??????????????????
6/10(?) ?? lt??gt
6/17(?) ?? ??????????(????????????)
6/24(?) ?? ??????????(???????????) ????????????
7/1(?) ?? ??????????(????) ????????????????????
7/8(?) ?? ????????(??1)
7/15(?) ?? ????????(??2)
7/22(?) ?? lt??gt
3
????4???????
?????????????????????????
??MAALSSAAVTIPSMAPSAPGRRRMRSSLV
(1)?????????(??????)???????????????????????
??MATVTSTTBAIPSFSGLKTNAATKVSAMA
(2)?????????????????????
(3)??????????????????????????????????
???MAALSSAAVSVPSFAAATPMRSSRSSRMV
???MAAITSATVTIPSFTGLKLAVSSKPKTLS
(4)??????????????????
(5)?????????????????
4
???????????
5
??????????????
????
DNA??
??????
???? ????
????
DNA?????????????????????(??????)
atgacggacaaattgacctcccttcgtcagtacaccaccgtagtggccga
c
M T D K L T S L R Q Y T T V V A D T G D
6
??????DNA?????????????
??????????DNA????????????????? ???????????????????
?????? ????DNA??????? ??????????????
???????????????????????? ????????????
7
??????????????????????
?????????????( Triosephosphate isomerase (EC
5.3.1.1) (TIM,TPIS))
gtTPIS_HUMAN ?? "Triosephosphate isomerase (EC
5.3.1.1) (TIM) (Triose-phosphateisomerase)" APSRKF
FVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPT AYIDFARQKL
DPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATW VVLGHSERRHVFGE
SDELIGQKVAHALAEGLGVIACIGEKLDERE AGITEKVVFEQTKVIADN
VKDWSKVVLAYEPVWAIGTGKTATPQQ AQEVHEKLRGWLKSNVSDAVAQ
STRIIYGGSVTGATCKELASQPD VDGFLVGGASLKPEFVDIINAKQ
gtTPIS_RABIT ??? "Triosephosphate isomerase (EC
5.3.1.1) (TIM) (Triose-phosphateisomerase)" APSRKF
FVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPT AYIDFARQKL
DPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATW VVLGHSERRHVFGE
SDELIGQKVAHALSEGLGVIACIGEKLDERE AGITEKVVFEQTKVIADN
VKDWSKVVLAYEPVWAIGTGKTATPQQ AQEVHEKLRGWLKSNVSDAVAQ
STRIIYGGSVTGATCKELASQPD VDGFLVGGASLKPEFVDIINAKQ
8
??????????????????????
?????????????( Triosephosphate isomerase (EC
5.3.1.1) (TIM,TPIS))
gtTPIS_HUMAN ?? "Triosephosphate isomerase (EC
5.3.1.1) (TIM) (Triose-phosphateisomerase)" APSRKF
FVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPT AYIDFARQKL
DPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATW VVLGHSERRHVFGE
SDELIGQKVAHALAEGLGVIACIGEKLDERE AGITEKVVFEQTKVIADN
VKDWSKVVLAYEPVWAIGTGKTATPQQ AQEVHEKLRGWLKSNVSDAVAQ
STRIIYGGSVTGATCKELASQPD VDGFLVGGASLKPEFVDIINAKQ
gtTPIS_YEAST ?? "Triosephosphate isomerase (EC
5.3.1.1) (TIM) (Triose-phosphateisomerase)" ARTFFV
GGNFKLNGSKQSIKEIVERLNTASIPENVEVVICPPATY LDYSVSLVKK
PQVTVGAQNAYLKASGAFTGENSVDQIKDVGAKWV ILGHSERRSYFHED
DKFIADKTKFALGQGVGVILCIGETLEEKKA GKTLDVVERQLNAVLEEV
KDWTNVVVAYEPVWAIGTGLAATPEDA QDIHASIRKFLASKLGDKAASE
LRILYGGSANGSNAVTFKDKADV DGFLVGGASLKPEFVDIINSRN
9
??????????????????????
?????????????( Triosephosphate isomerase (EC
5.3.1.1) (TIM,TPIS))
gtTPIS_HUMAN ?? "Triosephosphate isomerase (EC
5.3.1.1) (TIM) (Triose-phosphateisomerase)" APSRKF
FVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPT AYIDFARQKL
DPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATW VVLGHSERRHVFGE
SDELIGQKVAHALAEGLGVIACIGEKLDERE AGITEKVVFEQTKVIADN
VKDWSKVVLAYEPVWAIGTGKTATPQQ AQEVHEKLRGWLKSNVSDAVAQ
STRIIYGGSVTGATCKELASQPD VDGFLVGGASLKPEFVDIINAKQ
gtTPIS_ECOLI ??? "Triosephosphate isomerase (EC
5.3.1.1) (TIM) (Triose-phosphateisomerase)" MRHPLV
MGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEM YIDMAKREAE
GSHIMLGAQNVDLNLSGAFTGETSAAMLKDIGAQY IIIGHSERRTYHKE
SDELIAKKFAVLKEQGLTPVLCIGETEAENE AGKTEEVCARQIDAVLKT
QGAAAFEGAVIAYEPVWAIGTGKSATP AQAQAVHKFIRDHIAKVDANIA
EQVIIQYGGSVNASNAAELFAQP DIDGALVGGASLKADAFAVIVKAAEA
AKQA
10
???????? ?? ? ?????
?????????????( Triosephosphate isomerase (EC
5.3.1.1) (TIM,TPIS))???
??(TPIS_HUMAN)????(TPIS_RABIT)??? HUMAN
1APSRKFFVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPTAYI
DFARQKLDPKIA60
RABIT
1APSRKFFVGGNWKMNGRKKNLGELITTLNAAKVPADTEVVCAPPTAYI
DFARQKLDPKIA60 TPIS_HUMAN 248 vs TPIS_RABIT 248
SeqID 98.4 ??(TPIS_HUMAN)????(TPIS_ECOLI)???
HUMAN 4RKFFVGGNWKMNGRKQSLGELIGTLNAAKVP-ADTEVVCA
PPTAYIDFARQKLD-PKIAV61
ECOLI
2RHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDM
AKREAEGSHIML61 TPIS_HUMAN 248 vs TPIS_ECOLI
255 SeqID 45.9
??(substitution) ??????????
?????(insertion, deletion indel)
11
?????????????
??????????a??ß? (SeqID 46.0)
Alpha 2LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYF
PHF-DLS-----HGSAQV55
Beta
3LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDL
STPDAVMGNPKV60 Alpha 56KGHGKKVADALTNAVAHVDDMPNA
LSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPA11

Beta 61KAHGKKVLGAFSDGLAHLDNLKGTFATLSELH
CDKLHVDPENFRLLGNVLVCVLAHHFGK120 Alpha
116EFTPAVHASLDKFLASVSTVLTSKY140
Beta 121EFTPPVQAAYQKVVAGVAN
ALAHKY145
???????? ??????
??????????????????????
12
????(???????)?????
?????????????????????????
??(similarity) ??(homology)??????????????????
(????????????????????????) ??(analogy)
????????????
13
??????????
???????????(??????)??????????
???????
???
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??
??
??
??
???
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???
???
???
14
2????????????

• ????????????
• ????????????????????
• ??????
• ??????????????????

ACFDE ACEEE
3??????3?? F?E????D?E???????????
BCDEF ABEEFG
ABCDEF CDE
ABCDEF --CDE-
-BCDEF- AB-EEFG
??????????????????
15
????????

• (1)????????

???????DNA??????????? BLAST???????????a1,ß-3
??????????????????? L(????,???) ? V(???????)
?????? L(????,???) ? E(???????-??)
??????
16
(2)????????(log odds score)
2??????????????????????A,B???????
Protein1 XXXXAXXXX Protein2 XXXXBXXXX
Pevo(A,B) ????????A?B?????????
Prand(A)Prand(B) ???A?B??????????
17
BLOSUM62 (blastp????????????????????) A R
N D C Q E G H I L K M F P S T W Y
V B Z X A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1
-1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 R -1 5
0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2
-3 -1 0 -1 -4 N -2 0 6 1 -3 0 0 0 1 -3
-3 0 -2 -3 -2 1 0 -4 -2 -3 3 0 -1 -4 D -2
-2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1
-4 -3 -3 4 1 -1 -4 C 0 -3 -3 -3 9 -3 -4 -3
-3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4
Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1
0 -1 -2 -1 -2 0 3 -1 -4 E -1 0 0 2 -4 2 5
-2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 4 -1
-4 G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3
-2 0 -2 -2 -3 -3 -1 -2 -1 -4 H -2 0 1 -1 -3
0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 0
-1 -4 I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1
0 -3 -2 -1 -3 -1 3 -3 -3 -1 -4 L -1 -2 -3 -4 -1
-2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4
-3 -1 -4 K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5
-1 -3 -1 0 -1 -3 -2 -2 0 1 -1 -4 M -1 -1 -2
-3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1
1 -3 -1 -1 -4 F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0
-3 0 6 -4 -2 -2 1 3 -1 -3 -3 -1 -4 P -1 -2
-2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4
-3 -2 -2 -1 -2 -4 S 1 -1 1 0 -1 0 0 0 -1
-2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 0 0 -4 T
0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5
-2 -2 0 -1 -1 0 -4 W -3 -3 -4 -4 -2 -2 -3 -2
-2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -3 -2 -4
Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3
-2 -2 2 7 -1 -3 -2 -1 -4 V 0 -3 -3 -3 -1 -2
-2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 -2
-1 -4 B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3
-3 -2 0 -1 -4 -3 -3 4 1 -1 -4 Z -1 0 0 1
-3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2
1 4 -1 -4 X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1
-1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 -4 -4 -4
-4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4
-4 -4 -4 -4 1
18
???????
AFDC AEEC
S(A,A) S(F,E) S(D,E) S(C,C) 12 4
-3 2 9
??????????????????(?????????)?????
AFDGC AEE-C
S(A,A) S(F,E) S(D,E) gap S(C,C) 10 4
-3 2 -2 9

19
??????
?????(???????)???????????????????

1. ????????????
2. ????????????

AFAED-C A--EEGC
AFDC AEEC
??????
??????

1. ??????????? (ClustalW)
2. ?????????? (FASTA, BLAST)

ACDEFGHK-LM A---FGHKKL-
ACDEFGHKLM AFGHKKL
FGHK-L FGHKKL
?????
????
?????????????????? ???????????????????????????
20
????????? ?1 (1)
??????1????0?????-1????
??1
1GCTAGACTCG 2AGCTAGACTC
G
C
T
G
A
C
T
C
G
A
A
G
(1)??1???2? ???????
C
T
A
??2
G
A
C
T
C
21
????????? ?1 (2)
??????1????0?????-1????
??1
1GCTAGACTCG 2AGCTAGACTC
G
C
T
G
A
C
T
C
G
A
A
G
(1)??1???2? ???????
C
T
(2)??????? ???????
A
??2
G
A
C
T
C
22
????????? ?1 (3)
??????1????0?????-1????
??1
1GCTAGACTCG 2AGCTAGACTC
G
C
T
G
A
C
T
C
G
A
A
G
(1)??1???2? ???????
C
T
(2)??????? ???????
A
??2
G
(3)?????????? ???????????
A
C
T
C
23
????????? ?1 (4)
??????1????0?????-1????
??1
1GCTAGACTCG 2AGCTAGACTC
G
C
T
G
A
C
T
C
G
A
A
G
(1)??1???2? ???????
C
T
(2)??????? ???????
A
??2
G
(3)?????????? ???????????
A
C
(4)??????
T
1-GCTAGACTCG 2AGCTAGACTC-
C
?????(1)9???(0)0????(-1)27
24
????????? ?2 (1)
??????1????0?????-1????
??1
??1GCTCGACTTG ??2GCACGCTATG
G
C
T
G
A
C
T
T
G
C
G
C
(1)??1???2? ???????
A
C
G
??2
C
T
A
T
G
25
????????? ?2 (2)
??????1????0?????-1????
??1
??1GCTCGACTTG ??2GCACGCTATG
G
C
T
G
A
C
T
T
G
C
G
C
(1)??1???2? ???????
A
C
(2)??????? ???????
G
??2
C
T
A
T
G
26
????????? ?2 (3)
??????1????0?????-1????
??1
??1GCTCGACTTG ??2GCACGCTATG
G
C
T
G
A
C
T
T
G
C
G
C
(1)??1???2? ???????
A
C
(2)??????? ???????
G
??2
C
(3)?????????? ???????????
T
A
T
G
27
????????? ?2 (4)
??????1????0?????-1????
??1
??1GCTCGACTTG ??2GCACGCTATG
G
C
T
G
A
C
T
T
G
C
G
C
(1)??1???2? ???????
A
C
(2)??????? ???????
G
??2
C
(3)?????????? ???????????
T
A
(4)??????
T
1GCTCGACT-TG 2GCACG-CTATG
G
?????(1)8???(0)1????(-1)26
28
????????????????
??1GATTGCCGA ??2GATTGCGA
29
???????????
HBB_HUMAN
HBA_HUMAN
MatrixBLOSUM62, W7,T10
MatrixID,W5,T3
MatrixID,W1,T1
???????????????? ? ??W ?word??????T ???????????
W
??????????????????? ????????????????????
30
?????????????

• ?????????
• ??????????????
• ?????????????????????????
• ??????????????????????????(??????)??????

31
??????????????

• ?????????????????????????
• ??????????????????(Dynamic Programming)???????????
  ?????
• O(NM)????(?????????)

32
??????
??A????L?????????????? ??????????
33
???????????????????

• ??????????????????
• ?????????????????????????????????????
• ?????????????????????????

j
??
i
??
34
??????????????(Needleman Wunsh,1970)
??
(0)??
??????????????????0???
(1)???????
??
(2)????????
??????????????????????
35
?????????
(1)Forward
(2)TraceBack
LDGV LQ-I
O(NM)
36
?????????????????
????
?????
37
?????????????(Smith Waterman,1981)
(0)??
?????????0???
(1)???????
(2)????????
??????????????????????????????0???????
38
???????

• - BLAST?????? -

39
???????
???????????????????????????
?????
ALLGMFPVEQRSTD ALL-MYPVEQRTTE
ALLGMFPVEQRSTD
?????
????? (?????????)
????????

• ????????????(???????)
• ????????????????????
• ??????
• ????????????????????
• ?????
• ???????????????????????????

40
??????????????????????????????????
? ?????????????????

• ??????????????
• ??????O(NM)?????
• 1,000100,000?????????????
• ? ?????????????????
• ?????????????????
• ????????????????
• ?????()? ????
• ?????????????

41
BLAST?????????????
???????????????????????????????
???????????????????????????????????
????????????????????????
153?????????5977??????????????????(Pentium4)
?????DP 16.989 sec
SSEARCH 2.911 sec
FASTA(ktup1) 1.226 sec
FASTA(ktup2) 0.608 sec
BLASTP 0.118 sec
42
????????
(1)Forward
(2)TraceBack
LDGV LQ-I
O(NM)
43
BLAST???????????
??SmithWaterman????????????DP????

1. ?????word?????word???????
2. ??word????????????????
3. ?????word?ungap???(HSP)
4. ???gap???????????

44
BLASTP 2.2.1 Apr-13-2001 Reference Altschul,
Stephen F., Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb
Miller, and David J. Lipman (1997), "Gapped
BLAST and PSI-BLAST a new generation of protein
database search programs", Nucleic Acids Res.
253389-3402. Query RECA_ECOLI "RecA protein
(Recombinase A)" (352 letters) Database
40scop1.59nm 3886 sequences 705,110
total letters Searching........done

Score E Sequences producing significant
alignments (bits)
Value 2reb-1 c.37.1.11 RECA PROTEIN
(E.C.3.4.99.37) 448
e-127 1g18A2 d.48.1.1 RECA PROTEIN
70 9e-14 1g0uF
d.153.1.4 PROTEASOME COMPONENT C1
32 0.020 1byrA d.136.1.1
ENDONUCLEASE
28 0.29 1g3qA c.37.1.10 CELL DIVISION
INHIBITOR 28
0.38 1ct5A c.1.6.2 YEAST HYPOTHETICAL PROTEIN,
SELENOMET 28 0.49 1g0uD
d.153.1.4 PROTEASOME COMPONENT PUP2
27 1.1 1e32A2 c.37.1.13 P97
26
1.4 1g0uA d.153.1.4 PROTEASOME COMPONENT Y7
26 1.9 1cp2A
c.37.1.10 NITROGENASE IRON PROTEIN
26 1.9 1f3oA c.37.1.12
HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN
25 2.4 1qj2B2 d.133.1.1 CARBON MONOXIDE
DEHYDROGENASE 25 3.2 1dgyA
c.72.1.1 ADENOSINE KINASE
25 3.2 1skyB3 c.37.1.11
F1-ATPASE
25 3.2 1g6oA c.37.1.13 CAG-ALPHA
25 4.2 1cmxA
d.3.1.6 UBIQUITIN YUH1-UBAL
24 7.1 8abp- c.93.1.1
L-ARABINOSE-BINDING PROTEIN (MUTANT WITH MET
1... 24 7.1 2tpsA c.1.3.1 THIAMIN PHOSPHATE
SYNTHASE 24
7.1 1b8aA1 b.40.4.1 ASPARTYL-TRNA SYNTHETASE
24 7.1 1qtsA1
b.1.10.1 AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT
(ALPHA- 24 7.1 1b15A c.2.1.2 ALCOHOL
DEHYDROGENASE 23
9.3 1pmi- b.82.1.3 PHOSPHOMANNOSE ISOMERASE
23 9.3 gt2reb-1
c.37.1.11 RECA PROTEIN (E.C.3.4.99.37)
Length 243 Score 448 bits (1152), Expect
e-127 Identities 243/266 (91), Positives
243/266 (91), Gaps 23/266 (8) Query 3
DENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALG
AGGLPMGRIV 62 DENKQKALAAALGQIEKQFGKGSIM
RLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIV Sbjct 1
DENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALG
AGGLPMGRIV 60 Query 63 EIYGPESSGKTTLTLQVIAAAQRE
GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTG 122
EIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVD
IDNLLCSQPDTG Sbjct 61 EIYGPESSGKTTLTLQVIAAAQREGK
TCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTG 120 Query
123 EQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAA
RMMSQAMRKLAGNL 182 EQALEICDALARSGAVDVIV
VDSVAALTPKAEIE GLAARMMSQAMRKLAGNL Sbjct
121 EQALEICDALARSGAVDVIVVDSVAALTPKAEIE--------GLAA
RMMSQAMRKLAGNL 172 Query 183 KQSNTLLIFINQIRMKIGV
MFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSET 242
KQSNTLLIFINQ
TGGNALKFYASVRLDIRRIGAVKEGENVVGSET Sbjct 173
KQSNTLLIFINQ---------------TGGNALKFYASVRLDIRRIGAVK
EGENVVGSET 217 Query 243 RVKVVKNKIAAPFKQAEFQILYG
EGI 268 RVKVVKNKIAAPFKQAEFQILYGEGI Sbjc
t 218 RVKVVKNKIAAPFKQAEFQILYGEGI 243
BLAST? ???(1)
45
BLASTP 2.2.1 Apr-13-2001 Reference Altschul,
Stephen F., Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb
Miller, and David J. Lipman (1997), "Gapped
BLAST and PSI-BLAST a new generation of protein
database search programs", Nucleic Acids Res.
253389-3402. Query RECA_ECOLI "RecA protein
(Recombinase A)" (352 letters) Database
40scop1.59nm 3886 sequences 705,110
total letters Searching........done

Score E Sequences producing significant
alignments (bits)
Value 2reb-1 c.37.1.11 RECA PROTEIN
(E.C.3.4.99.37) 448
e-127 1g18A2 d.48.1.1 RECA PROTEIN
70 9e-14 1g0uF
d.153.1.4 PROTEASOME COMPONENT C1
32 0.020 1byrA d.136.1.1
ENDONUCLEASE
28 0.29 1g3qA c.37.1.10 CELL DIVISION
INHIBITOR 28
0.38 1ct5A c.1.6.2 YEAST HYPOTHETICAL PROTEIN,
SELENOMET 28 0.49 1g0uD
d.153.1.4 PROTEASOME COMPONENT PUP2
27 1.1 1e32A2 c.37.1.13 P97
26
1.4 1g0uA d.153.1.4 PROTEASOME COMPONENT Y7
26 1.9 1cp2A
c.37.1.10 NITROGENASE IRON PROTEIN
26 1.9 1f3oA c.37.1.12
HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN
25 2.4 1qj2B2 d.133.1.1 CARBON MONOXIDE
DEHYDROGENASE 25 3.2 1dgyA
c.72.1.1 ADENOSINE KINASE
25 3.2 1skyB3 c.37.1.11
F1-ATPASE
25 3.2 1g6oA c.37.1.13 CAG-ALPHA
25 4.2 1cmxA
d.3.1.6 UBIQUITIN YUH1-UBAL
24 7.1 8abp- c.93.1.1
L-ARABINOSE-BINDING PROTEIN (MUTANT WITH MET
1... 24 7.1 2tpsA c.1.3.1 THIAMIN PHOSPHATE
SYNTHASE 24
7.1 1b8aA1 b.40.4.1 ASPARTYL-TRNA SYNTHETASE
24 7.1 1qtsA1
b.1.10.1 AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT
(ALPHA- 24 7.1 1b15A c.2.1.2 ALCOHOL
DEHYDROGENASE 23
9.3 1pmi- b.82.1.3 PHOSPHOMANNOSE ISOMERASE
23 9.3 gt2reb-1
c.37.1.11 RECA PROTEIN (E.C.3.4.99.37)
Length 243 Score 448 bits (1152), Expect
e-127 Identities 243/266 (91), Positives
243/266 (91), Gaps 23/266 (8) Query 3
DENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALG
AGGLPMGRIV 62 DENKQKALAAALGQIEKQFGKGSIM
RLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIV Sbjct 1
DENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALG
AGGLPMGRIV 60 Query 63 EIYGPESSGKTTLTLQVIAAAQRE
GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTG 122
EIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVD
IDNLLCSQPDTG Sbjct 61 EIYGPESSGKTTLTLQVIAAAQREGK
TCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTG 120 Query
123 EQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAA
RMMSQAMRKLAGNL 182 EQALEICDALARSGAVDVIV
VDSVAALTPKAEIE GLAARMMSQAMRKLAGNL Sbjct
121 EQALEICDALARSGAVDVIVVDSVAALTPKAEIE--------GLAA
RMMSQAMRKLAGNL 172 Query 183 KQSNTLLIFINQIRMKIGV
MFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSET 242
KQSNTLLIFINQ
TGGNALKFYASVRLDIRRIGAVKEGENVVGSET Sbjct 173
KQSNTLLIFINQ---------------TGGNALKFYASVRLDIRRIGAVK
EGENVVGSET 217 Query 243 RVKVVKNKIAAPFKQAEFQILYG
EGI 268 RVKVVKNKIAAPFKQAEFQILYGEGI Sbjc
t 218 RVKVVKNKIAAPFKQAEFQILYGEGI 243 gt1g18A2
d.48.1.1 RECA PROTEIN Length 60
Score 70.1 bits (170), Expect 9e-14
Identities 30/56 (53), Positives 44/56
(78) Query 272 GELVDLGVKEKLIEKAGAWYSYKGEKIGQGKA
NATAWLKDNPETAKEIEKKVRELL 327 G LDGV
LI KGAWYGEGQGK NA L N A EIEKKE
L Sbjct 4 GSLIDMGVDQGLIRKSGAWFTYEGEQLGQGKENARNF
LVENADVADEIEKKIKEKL 59 gt1g0uF d.153.1.4
PROTEASOME COMPONENT C1 Length 242
Score 32.3 bits (72), Expect 0.020
Identities 25/88 (28), Positives 47/88
(53), Gaps 9/88 (10) Query 271
YGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKANATAWLK----DNPE--
TAKEIEKKVR 324 G G E G
YKG GG A A L PE AE K Sbjct 132
FGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGL
SAREAVKQAA 191 Query 325 EL--LLSNPNSTPDFSVDDSE-G
VAETN 349 L N DF S
ETN Sbjct 192 KIIYLAHEDNKEKDFELEISWCSLSETN
219 gt1byrA d.136.1.1 ENDONUCLEASE
Length 152 Score 28.5 bits (62), Expect
0.29 Identities 28/102 (27), Positives
46/102 (44), Gaps 19/102 (18) Query 65
YGPESSGKTTLTLQVIAAAQREGKTCAFI----DAEHALDPIYARKLGVD
IDNLLCSQPD 120 Y PE S L L I A
A D AL AK GVD Sbjct 8
YSPEGSARV-LVLSAIDSAKTSIRMMAYSFTAPDIMKAL--VAAKKRGVD
VKIVIDERGN 64 Query 121 TGEQALEICDALARSGAV------
------DVIVVDSVAALT 150 TG A
SG VIVDV T Sbjct 65
TGRASIAAMNYIANSGIPLRTDSNFPIQHDKVIIVDNVTVET
106 gt1g3qA c.37.1.10 CELL DIVISION INHIBITOR
Length 237 Score 28.1 bits (61),
Expect 0.38 Identities 21/71 (29),
Positives 34/71 (47), Gaps 2/71 (2) Query
58 MGRIVEIY-GPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPI
YARKLGVDIDNLLC 116 MGRI I G
GKTTT A G D LGVD
Sbjct 1 MGRIISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVD
GDLTMANL-SLVLGVDDPDVTL 59 Query 117 SQPDTGEQALE
127 GE E Sbjct 60 HDVLAGEANVE
70 gt1ct5A c.1.6.2 YEAST HYPOTHETICAL PROTEIN,
SELENOMET Length 228 Score 27.7
bits (60), Expect 0.49 Identities 28/103
(27), Positives 48/103 (46), Gaps 4/103
(3) Query 237 VVGSETR-VKVVKNKIAAPFKQAEFQILYGEGI
NFYGE--LVDLGVKEKLIEKAGAWYSY 293 VV E
VK QILY G GE L K KL
W Sbjct 23 VVNAEAKNVKILLLVVSKLKPASDIQILYDHGVR
EFGENYVQELIEKAKLLPDDIKWHFI 82 Query 294
KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLSNPNSTPD 336
G K A ET KK L S
PD Sbjct 83 GGLQTNKCKDLAKVPNLYSVETIDSL-KKAKKLNES
RAKFQPD 124 gt1g0uD d.153.1.4 PROTEASOME
COMPONENT PUP2 Length 230 Score
26.6 bits (57), Expect 1.1 Identities 20/67
(29), Positives 30/67 (43), Gaps 3/67
(4) Query 264 YGEGINFYGELVDLGVKEKLIEKAGAWYSYKGE
KIGQGKANATAWLKD---NPETAKEIE 320 G
G D G E G Y Y IG G A A L T
KE E Sbjct 118 FGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKA
IGSGSEGAQAELLNEWHSSLTLKEAE 177 Query 321
KKVRELL 327 V L Sbjct 178 LLVLKIL
184 gt1e32A2 c.37.1.13 P97 Length
258 Score 26.2 bits (56), Expect 1.4
Identities 33/136 (24), Positives 55/136
(40), Gaps 26/136 (19) Query 55
GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYA
RKLGVDIDNL 114 G R YGP GKT
A A G I G I Sbjct 34
GVKPPRGILLYGPPGTGKTLIAR---AVANETGAFFFLIN----------
---GPEIMSK 77 Query 115 LCSQPDTGEQALEICDALARSGAV
DVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQA 174
L E L A A I D A PK E
H RSQ Sbjct 78 LAGE---SESNLRKAFEEAEKNAPA
IIFIDELDAIAPKRE------KTHGEVERRIVSQL 128 Query
175 MRKLAGNLKQSNTLLI 190 G LKQ
Sbjct 129 LTLMDG-LKQRAHVIV 143 gt1g0uA
d.153.1.4 PROTEASOME COMPONENT Y7
Length 246 Score 25.8 bits (55), Expect
1.9 Identities 15/61 (24), Positives 30/61
(48), Gaps 1/61 (1) Query 284
IEKAGAWYSYKGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLSNPNS
TP-DFSVDDS 342 G K IGG A
L EE LL S F D Sbjct 146
VDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKES
VEGEFNGDTI 205 Query 343 E 343
E Sbjct 206 E 206 gt1cp2A c.37.1.10
NITROGENASE IRON PROTEIN Length 269
Score 25.8 bits (55), Expect 1.9 Identities
22/86 (25), Positives 39/86 (44), Gaps
2/86 (2) Query 60 RIVEIYGPESSGKTTLTLQVIAAAQREG
KTCAFIDAEHALDPIYARKLGVDIDNLLCSQP 119 R
V IYG GKT T GKT D G
L Sbjct 2 RQVAIYGKGGIGKSTTTQNLTSGLHAMGKT
IMVVGCDPKADSTRLLLGGLAQKSVLDTLR 61 Query 120
DTGEQALEICDALARSGAVDVIVVDS 145 GE
E D G VS Sbjct 62
EEGED-VEL-DSILKEGYGGIRCVES 85 gt1f3oA
c.37.1.12 HYPOTHETICAL ABC TRANSPORTER
ATP-BINDING PROTEIN Length
232 Score 25.4 bits (54), Expect 2.4
Identities 13/36 (36), Positives 19/36
(52), Gaps 1/36 (2) Query 59
GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID 94
G V I GP SGKT L I ID Sbjct 31
GEFVSIMGPSGSGKSTM-LNIIGCLDKPTEGEVYID 65 gt1qj2B2
d.133.1.1 CARBON MONOXIDE DEHYDROGENASE
Length 662 Score 25.0 bits (53), Expect
3.2 Identities 17/49 (34), Positives 26/49
(52), Gaps 1/49 (2) Query 230
AVKEGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLG
278 AK VG K K A FK E
G GIF EV G Sbjct 299 AMKKAMDTVGYHQLRAEQKAKQEA
-FKRGETREIMGIGISFFTEIVGAG 346 gt1dgyA c.72.1.1
ADENOSINE KINASE Length 333 Score
25.0 bits (53), Expect 3.2 Identities 26/118
(22), Positives 50/118 (42), Gaps 3/118
(2) Query 159 IGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIF
INQIRMKIGVMFGNPETTTGGNALKFY 218 IG
L A S LK L QR NP
GGAL Sbjct 8 IGNPILDLVAEVPSSFLDEFF--LKRGDAT
LATPEQMRIYSTLDQFNPTSLPGGSALNSV 65 Query 219
ASVRLDIRRIGAVKEGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGI
NFYGELVD 276 V R G G R
VK F G L Sbjct 66
RVVQKLLRKPGSAGY-MGAIGDDPRGQVLKELCDKEGLATRFMVAPGQST
GTCAVLIN 122 gt1skyB3 c.37.1.11 F1-ATPASE
Length 276 Score 25.0 bits (53),
Expect 3.2 Identities 15/62 (24), Positives
28/62 (44), Gaps 3/62 (4) Query 32
DRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIA
AAQREGKTCA 91 DR E TG D G
G I G GKT I C Sbjct 43
DRRSVHEPLQTGIKAIDALVPIG---RGQRELIIGDRQTGKTSVAIDTII
NQKDQNMICI 99 Query 92 FI 93
Sbjct 100 YV 101 gt1g6oA c.37.1.13
CAG-ALPHA Length 323 Score 24.6
bits (52), Expect 4.2 Identities 12/42
(28), Positives 21/42 (49) Query 55
GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE 96
G G V G SGKTT E D
E Sbjct 162 GIAIGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIIS
IEDTE 203 gt1cmxA d.3.1.6 UBIQUITIN YUH1-UBAL
Length 214 Score 23.9 bits (50),
Expect 7.1 Identities 15/57 (26), Positives
24/57 (41) Query 108 GVDIDNLLCSQPDTGEQALEICDA
LARSGAVDVIVVDSVAALTPKAEIEGEIGDSHM 164
G DDN L SQ DT D VI T E
D Sbjct 89 GSDLDNFLKSQSDTSSSKNRFDDVTTDQFVL
NVIKENVQTFSTGQSEAPEATADTNL 145 gt8abp-
c.93.1.1 L-ARABINOSE-BINDING PROTEIN (MUTANT
WITH MET 108 REPLACED Length
305 Score 23.9 bits (50), Expect 7.1
Identities 15/42 (35), Positives 24/42
(56), Gaps 3/42 (7) Query 103
YARKLGVDI--DNLLCSQPDTGEQALEICDALARSGAVDVIV 142
A K G D PD GE L DLA SGA
Sbjct 22 FADKAGKDLGFEVIKIAVPD-GEKTLNAIDSLAASG
AKGFVI 62 gt2tpsA c.1.3.1 THIAMIN PHOSPHATE
SYNTHASE Length 226 Score 23.9
bits (50), Expect 7.1 Identities 22/70
(31), Positives 30/70 (42), Gaps 17/70
(24) Query 121 TGEQALEICD---ALARSGAVDVIVVDSVA-A
LTPKA-------------EIEGEIGDSH 163 TGE
A R V IV D V AL KA E
IGD Sbjct 58 TGEARIKFAEKAQAACREAGVPFIVNDDVELAL
NLKADGIHIGQEDANAKEVRAAIGDMI 117 Query 164
MGLAARMMSQ 173 GA MS Sbjct 118
LGVSAHTMSE 127 gt1b8aA1 b.40.4.1 ASPARTYL-TRNA
SYNTHETASE Length 103 Score 23.9
bits (50), Expect 7.1 Identities 11/33
(33), Positives 19/33 (57) Query 127
EICDALARSGAVDVIVVDSVAALTPKAEIEGEI 159
E DV V V TPKA EI Sbjct 58
ELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEI 90 gt1qtsA1
b.1.10.1 AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT
(ALPHA- Length 133 Score 23.9
bits (50), Expect 7.1 Identities 14/58
(24), Positives 27/58 (46), Gaps 2/58
(3) Query 267 GINFYGELVDLGVKEKLIEKAGAWYSYKGEKIG
QGKANATAWL--KDNPETAKEIEKK 322 G F
L GK G G K N T L D T
K Sbjct 23 GVLFENQLLQIGLKSEFRQNLGRMFIFYGNKTST
QFLNFTPTLICADDLQTNLNLQTK 80 gt1b15A c.2.1.2
ALCOHOL DEHYDROGENASE Length 254
Score 23.5 bits (49), Expect 9.3 Identities
9/19 (47), Positives 14/19 (73) Query 318
EIEKKVRELLLSNPNSTPD 336 E V ELLLSP
T Sbjct 197 DVEPRVAELLLSHPTQTSE 215 gt1pmi-
b.82.1.3 PHOSPHOMANNOSE ISOMERASE
Length 440 Score 23.5 bits (49), Expect
9.3 Identities 16/60 (26), Positives 23/60
(37) Query 281 EKLIEKAGAWYSYKGEKIGQGKANATAWLKDN
PETAKEIEKKVRELLLSNPNSTPDFSVD 340 EKL
Y KIG A A P K EL S P
D Sbjct 3 EKLFRIQCGYQNYDWGKIGSSSAVAQFVHNSDPS
ITIDETKPYAELWMGTHPSVPSKAID 62 Database
40scop1.59nm Posted date Jun 22, 2002 306
PM Number of letters in database 705,110
Number of sequences in database 3886 Lambda
K H 0.314 0.134 0.367
Gapped Lambda K H 0.267 0.0410
0.140 Matrix BLOSUM62 Gap Penalties
Existence 11, Extension 1 Number of Hits to DB
483,807 Number of Sequences 3886 Number of
extensions 19667 Number of successful
extensions 69 Number of sequences better than
10.0 22 Number of HSP's better than 10.0 without
gapping 15 Number of HSP's successfully gapped
in prelim test 7 Number of HSP's that attempted
gapping in prelim test 52 Number of HSP's gapped
(non-prelim) 22 length of query 352 length of
database 705,110 effective HSP length
79 effective length of query 273 effective
length of database 398,116 effective search
space 108685668 effective search space used
108685668 T 11 A 40 X1 16 ( 7.2 bits) X2 38
(14.6 bits) X3 64 (24.7 bits) S1 42 (21.9
bits) S2 49 (23.5 bits)
BLAST? ???(2)
46
BLASTP 2.2.1 Apr-13-2001 Reference Altschul,
Stephen F., Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb
Miller, and David J. Lipman (1997), "Gapped
BLAST and PSI-BLAST a new generation of protein
database search programs", Nucleic Acids Res.
253389-3402. Query RECA_ECOLI "RecA protein
(Recombinase A)" (352 letters) Database
40scop1.59nm 3886 sequences 705,110
total letters Searching........done

Score E Sequences producing significant
alignments (bits)
Value 2reb-1 c.37.1.11 RECA PROTEIN
(E.C.3.4.99.37) 448
e-127 1g18A2 d.48.1.1 RECA PROTEIN
70 9e-14 1g0uF
d.153.1.4 PROTEASOME COMPONENT C1
32 0.020 1byrA d.136.1.1
ENDONUCLEASE
28 0.29 1g3qA c.37.1.10 CELL DIVISION
INHIBITOR 28
0.38 1ct5A c.1.6.2 YEAST HYPOTHETICAL PROTEIN,
SELENOMET 28 0.49 1g0uD
d.153.1.4 PROTEASOME COMPONENT PUP2
27 1.1 1e32A2 c.37.1.13 P97
26
1.4 1g0uA d.153.1.4 PROTEASOME COMPONENT Y7
26 1.9 1cp2A
c.37.1.10 NITROGENASE IRON PROTEIN
26 1.9 1f3oA c.37.1.12
HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN
25 2.4 1qj2B2 d.133.1.1 CARBON MONOXIDE
DEHYDROGENASE 25 3.2 1dgyA
c.72.1.1 ADENOSINE KINASE
25 3.2 1skyB3 c.37.1.11
F1-ATPASE
25 3.2 1g6oA c.37.1.13 CAG-ALPHA
25 4.2 1cmxA
d.3.1.6 UBIQUITIN YUH1-UBAL
24 7.1 8abp- c.93.1.1
L-ARABINOSE-BINDING PROTEIN (MUTANT WITH MET
1... 24 7.1 2tpsA c.1.3.1 THIAMIN PHOSPHATE
SYNTHASE 24
7.1 1b8aA1 b.40.4.1 ASPARTYL-TRNA SYNTHETASE
24 7.1 1qtsA1
b.1.10.1 AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT
(ALPHA- 24 7.1 1b15A c.2.1.2 ALCOHOL
DEHYDROGENASE 23
9.3 1pmi- b.82.1.3 PHOSPHOMANNOSE ISOMERASE
23 9.3 gt2reb-1
c.37.1.11 RECA PROTEIN (E.C.3.4.99.37)
Length 243 Score 448 bits (1152), Expect
e-127 Identities 243/266 (91), Positives
243/266 (91), Gaps 23/266 (8) Query 3
DENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALG
AGGLPMGRIV 62 DENKQKALAAALGQIEKQFGKGSIM
RLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIV Sbjct 1
DENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALG
AGGLPMGRIV 60 Query 63 EIYGPESSGKTTLTLQVIAAAQRE
GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTG 122
EIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVD
IDNLLCSQPDTG Sbjct 61 EIYGPESSGKTTLTLQVIAAAQREGK
TCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTG 120 Query
123 EQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAA
RMMSQAMRKLAGNL 182 EQALEICDALARSGAVDVIV
VDSVAALTPKAEIE GLAARMMSQAMRKLAGNL Sbjct
121 EQALEICDALARSGAVDVIVVDSVAALTPKAEIE--------GLAA
RMMSQAMRKLAGNL 172 Query 183 KQSNTLLIFINQIRMKIGV
MFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSET 242
KQSNTLLIFINQ
TGGNALKFYASVRLDIRRIGAVKEGENVVGSET Sbjct 173
KQSNTLLIFINQ---------------TGGNALKFYASVRLDIRRIGAVK
EGENVVGSET 217 Query 243 RVKVVKNKIAAPFKQAEFQILYG
EGI 268 RVKVVKNKIAAPFKQAEFQILYGEGI Sbjc
t 218 RVKVVKNKIAAPFKQAEFQILYGEGI 243 gt1g18A2
d.48.1.1 RECA PROTEIN Length 60
Score 70.1 bits (170), Expect 9e-14
Identities 30/56 (53), Positives 44/56
(78) Query 272 GELVDLGVKEKLIEKAGAWYSYKGEKIGQGKA
NATAWLKDNPETAKEIEKKVRELL 327 G LDGV
LI KGAWYGEGQGK NA L N A EIEKKE
L Sbjct 4 GSLIDMGVDQGLIRKSGAWFTYEGEQLGQGKENARNF
LVENADVADEIEKKIKEKL 59 gt1g0uF d.153.1.4
PROTEASOME COMPONENT C1 Length 242
Score 32.3 bits (72), Expect 0.020
Identities 25/88 (28), Positives 47/88
(53), Gaps 9/88 (10) Query 271
YGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKANATAWLK----DNPE--
TAKEIEKKVR 324 G G E G
YKG GG A A L PE AE K Sbjct 132
FGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGL
SAREAVKQAA 191 Query 325 EL--LLSNPNSTPDFSVDDSE-G
VAETN 349 L N DF S
ETN Sbjct 192 KIIYLAHEDNKEKDFELEISWCSLSETN
219 gt1byrA d.136.1.1 ENDONUCLEASE
Length 152 Score 28.5 bits (62), Expect
0.29 Identities 28/102 (27), Positives
46/102 (44), Gaps 19/102 (18) Query 65
YGPESSGKTTLTLQVIAAAQREGKTCAFI----DAEHALDPIYARKLGVD
IDNLLCSQPD 120 Y PE S L L I A
A D AL AK GVD Sbjct 8
YSPEGSARV-LVLSAIDSAKTSIRMMAYSFTAPDIMKAL--VAAKKRGVD
VKIVIDERGN 64 Query 121 TGEQALEICDALARSGAV------
------DVIVVDSVAALT 150 TG A
SG VIVDV T Sbjct 65
TGRASIAAMNYIANSGIPLRTDSNFPIQHDKVIIVDNVTVET
106 gt1g3qA c.37.1.10 CELL DIVISION INHIBITOR
Length 237 Score 28.1 bits (61),
Expect 0.38 Identities 21/71 (29),
Positives 34/71 (47), Gaps 2/71 (2) Query
58 MGRIVEIY-GPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPI
YARKLGVDIDNLLC 116 MGRI I G
GKTTT A G D LGVD
Sbjct 1 MGRIISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVD
GDLTMANL-SLVLGVDDPDVTL 59 Query 117 SQPDTGEQALE
127 GE E Sbjct 60 HDVLAGEANVE
70 gt1ct5A c.1.6.2 YEAST HYPOTHETICAL PROTEIN,
SELENOMET Length 228 Score 27.7
bits (60), Expect 0.49 Identities 28/103
(27), Positives 48/103 (46), Gaps 4/103
(3) Query 237 VVGSETR-VKVVKNKIAAPFKQAEFQILYGEGI
NFYGE--LVDLGVKEKLIEKAGAWYSY 293 VV E
VK QILY G GE L K KL
W Sbjct 23 VVNAEAKNVKILLLVVSKLKPASDIQILYDHGVR
EFGENYVQELIEKAKLLPDDIKWHFI 82 Query 294
KGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLSNPNSTPD 336
G K A ET KK L S
PD Sbjct 83 GGLQTNKCKDLAKVPNLYSVETIDSL-KKAKKLNES
RAKFQPD 124 gt1g0uD d.153.1.4 PROTEASOME
COMPONENT PUP2 Length 230 Score
26.6 bits (57), Expect 1.1 Identities 20/67
(29), Positives 30/67 (43), Gaps 3/67
(4) Query 264 YGEGINFYGELVDLGVKEKLIEKAGAWYSYKGE
KIGQGKANATAWLKD---NPETAKEIE 320 G
G D G E G Y Y IG G A A L T
KE E Sbjct 118 FGVALLIAGHDADDGYQLFHAEPSGTFYRYNAKA
IGSGSEGAQAELLNEWHSSLTLKEAE 177 Query 321
KKVRELL 327 V L Sbjct 178 LLVLKIL
184 gt1e32A2 c.37.1.13 P97 Length
258 Score 26.2 bits (56), Expect 1.4
Identities 33/136 (24), Positives 55/136
(40), Gaps 26/136 (19) Query 55
GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYA
RKLGVDIDNL 114 G R YGP GKT
A A G I G I Sbjct 34
GVKPPRGILLYGPPGTGKTLIAR---AVANETGAFFFLIN----------
---GPEIMSK 77 Query 115 LCSQPDTGEQALEICDALARSGAV
DVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQA 174
L E L A A I D A PK E
H RSQ Sbjct 78 LAGE---SESNLRKAFEEAEKNAPA
IIFIDELDAIAPKRE------KTHGEVERRIVSQL 128 Query
175 MRKLAGNLKQSNTLLI 190 G LKQ
Sbjct 129 LTLMDG-LKQRAHVIV 143 gt1g0uA
d.153.1.4 PROTEASOME COMPONENT Y7
Length 246 Score 25.8 bits (55), Expect
1.9 Identities 15/61 (24), Positives 30/61
(48), Gaps 1/61 (1) Query 284
IEKAGAWYSYKGEKIGQGKANATAWLKDNPETAKEIEKKVRELLLSNPNS
TP-DFSVDDS 342 G K IGG A
L EE LL S F D Sbjct 146
VDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKES
VEGEFNGDTI 205 Query 343 E 343
E Sbjct 206 E 206 gt1cp2A c.37.1.10
NITROGENASE IRON PROTEIN Length 269
Score 25.8 bits (55), Expect 1.9 Identities
22/86 (25), Positives 39/86 (44), Gaps
2/86 (2) Query 60 RIVEIYGPESSGKTTLTLQVIAAAQREG
KTCAFIDAEHALDPIYARKLGVDIDNLLCSQP 119 R
V IYG GKT T GKT D G
L Sbjct 2 RQVAIYGKGGIGKSTTTQNLTSGLHAMGKT
IMVVGCDPKADSTRLLLGGLAQKSVLDTLR 61 Query 120
DTGEQALEICDALARSGAVDVIVVDS 145 GE
E D G VS Sbjct 62
EEGED-VEL-DSILKEGYGGIRCVES 85 gt1f3oA
c.37.1.12 HYPOTHETICAL ABC TRANSPORTER
ATP-BINDING PROTEIN Length
232 Score 25.4 bits (54), Expect 2.4
Identities 13/36 (36), Positives 19/36
(52), Gaps 1/36 (2) Query 59
GRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFID 94
G V I GP SGKT L I ID Sbjct 31
GEFVSIMGPSGSGKSTM-LNIIGCLDKPTEGEVYID 65 gt1qj2B2
d.133.1.1 CARBON MONOXIDE DEHYDROGENASE
Length 662 Score 25.0 bits (53), Expect
3.2 Identities 17/49 (34), Positives 26/49
(52), Gaps 1/49 (2) Query 230
AVKEGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFYGELVDLG
278 AK VG K K A FK E
G GIF EV G Sbjct 299 AMKKAMDTVGYHQLRAEQKAKQEA
-FKRGETREIMGIGISFFTEIVGAG 346 gt1dgyA c.72.1.1
ADENOSINE KINASE Length 333 Score
25.0 bits (53), Expect 3.2 Identities 26/118
(22), Positives 50/118 (42), Gaps 3/118
(2) Query 159 IGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIF
INQIRMKIGVMFGNPETTTGGNALKFY 218 IG
L A S LK L QR NP
GGAL Sbjct 8 IGNPILDLVAEVPSSFLDEFF--LKRGDAT
LATPEQMRIYSTLDQFNPTSLPGGSALNSV 65 Query 219
ASVRLDIRRIGAVKEGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGI
NFYGELVD 276 V R G G R
VK F G L Sbjct 66
RVVQKLLRKPGSAGY-MGAIGDDPRGQVLKELCDKEGLATRFMVAPGQST
GTCAVLIN 122 gt1skyB3 c.37.1.11 F1-ATPASE
Length 276 Score 25.0 bits (53),
Expect 3.2 Identities 15/62 (24), Positives
28/62 (44), Gaps 3/62 (4) Query 32
DRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIA
AAQREGKTCA 91 DR E TG D G
G I G GKT I C Sbjct 43
DRRSVHEPLQTGIKAIDALVPIG---RGQRELIIGDRQTGKTSVAIDTII
NQKDQNMICI 99 Query 92 FI 93
Sbjct 100 YV 101 gt1g6oA c.37.1.13
CAG-ALPHA Length 323 Score 24.6
bits (52), Expect 4.2 Identities 12/42
(28), Positives 21/42 (49) Query 55
GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAE 96
G G V G SGKTT E D
E Sbjct 162 GIAIGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIIS
IEDTE 203 gt1cmxA d.3.1.6 UBIQUITIN YUH1-UBAL
Length 214 Score 23.9 bits (50),
Expect 7.1 Identities 15/57 (26), Positives
24/57 (41) Query 108 GVDIDNLLCSQPDTGEQALEICDA
LARSGAVDVIVVDSVAALTPKAEIEGEIGDSHM 164
G DDN L SQ DT D VI T E
D Sbjct 89 GSDLDNFLKSQSDTSSSKNRFDDVTTDQFVL
NVIKENVQTFSTGQSEAPEATADTNL 145 gt8abp-
c.93.1.1 L-ARABINOSE-BINDING PROTEIN (MUTANT
WITH MET 108 REPLACED Length
305 Score 23.9 bits (50), Expect 7.1
Identities 15/42 (35), Positives 24/42
(56), Gaps 3/42 (7) Query 103
YARKLGVDI--DNLLCSQPDTGEQALEICDALARSGAVDVIV 142
A K G D PD GE L DLA SGA
Sbjct 22 FADKAGKDLGFEVIKIAVPD-GEKTLNAIDSLAASG
AKGFVI 62 gt2tpsA c.1.3.1 THIAMIN PHOSPHATE
SYNTHASE Length 226 Score 23.9
bits (50), Expect 7.1 Identities 22/70
(31), Positives 30/70 (42), Gaps 17/70
(24) Query 121 TGEQALEICD---ALARSGAVDVIVVDSVA-A
LTPKA-------------EIEGEIGDSH 163 TGE
A R V IV D V AL KA E
IGD Sbjct 58 TGEARIKFAEKAQAACREAGVPFIVNDDVELAL
NLKADGIHIGQEDANAKEVRAAIGDMI 117 Query 164
MGLAARMMSQ 173 GA MS Sbjct 118
LGVSAHTMSE 127 gt1b8aA1 b.40.4.1 ASPARTYL-TRNA
SYNTHETASE Length 103 Score 23.9
bits (50), Expect 7.1 Identities 11/33
(33), Positives 19/33 (57) Query 127
EICDALARSGAVDVIVVDSVAALTPKAEIEGEI 159
E DV V V TPKA EI Sbjct 58
ELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEI 90 gt1qtsA1
b.1.10.1 AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT
(ALPHA- Length 133 Score 23.9
bits (50), Expect 7.1 Identities 14/58
(24), Positives 27/58 (46), Gaps 2/58
(3) Query 267 GINFYGELVDLGVKEKLIEKAGAWYSYKGEKIG
QGKANATAWL--KDNPETAKEIEKK 322 G F
L GK G G K N T L D T
K Sbjct 23 GVLFENQLLQIGLKSEFRQNLGRMFIFYGNKTST
QFLNFTPTLICADDLQTNLNLQTK 80 gt1b15A c.2.1.2
ALCOHOL DEHYDROGENASE Length 254
Score 23.5 bits (49), Expect 9.3 Identities
9/19 (47), Positives 14/19 (73) Query 318
EIEKKVRELLLSNPNSTPD 336 E V ELLLSP
T Sbjct 197 DVEPRVAELLLSHPTQTSE 215 gt1pmi-
b.82.1.3 PHOSPHOMANNOSE ISOMERASE
Length 440 Score 23.5 bits (49), Expect
9.3 Identities 16/60 (26), Positives 23/60
(37) Query 281 EKLIEKAGAWYSYKGEKIGQGKANATAWLKDN
PETAKEIEKKVRELLLSNPNSTPDFSVD 340 EKL
Y KIG A A P K EL S P
D Sbjct 3 EKLFRIQCGYQNYDWGKIGSSSAVAQFVHNSDPS
ITIDETKPYAELWMGTHPSVPSKAID 62 Database
40scop1.59nm Posted date Jun 22, 2002 306
PM Number of letters in database 705,110
Number of sequences in database 3886 Lambda
K H 0.314 0.134 0.367
Gapped Lambda K H 0.267 0.0410
0.140 Matrix BLOSUM62 Gap Penalties
Existence 11, Extension 1 Number of Hits to DB
483,807 Number of Sequences 3886 Number of
extensions 19667 Number of successful
extensions 69 Number of sequences better than
10.0 22 Number of HSP's better than 10.0 without
gapping 15 Number of HSP's successfully gapped
in prelim test 7 Number of HSP's that attempted
gapping in prelim test 52 Number of HSP's gapped
(non-prelim) 22 length of query 352 length of
database 705,110 effective HSP length
79 effective length of query 273 effective
length of database 398,116 effective search
space 108685668 effective search space used
108685668 T 11 A 40 X1 16 ( 7.2 bits) X2 38
(14.6 bits) X3 64 (24.7 bits) S1 42 (21.9
bits) S2 49 (23.5 bits)
BLAST? ???(3)
47
?????????????????
??????

• ?????()
• ??????????????30?????????????
• ????????????????????????????
• ???
• ????????????????????????????????????????
• E-value
• ???????????
• ??????????????????????????????????

48
E-value

• E-value ( expectation value)
• ??????????????????????
• ?????S????????????????????

????????????????????????????????
??????? ? ??????????? ??????? ?
???????????????
?????
?????????????????? ? ????????????? ?
?????????????????
?????
????????????????? ??0????????
????
?????1??????0.0001??0.01????
49
E-value????????????

• ???????K,?
• ???????????????????
• m???????
• n ??????????
• ?????????????????????? ???????

??????????????????E-value??? ???????????????????
???????? ?????E-value?????????
50
BLASTP 2.2.1 Apr-13-2001 Reference Altschul,
Stephen F., Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb
Miller, and David J. Lipman (1997), "Gapped
BLAST and PSI-BLAST a new generation of protein
database search programs", Nucleic Acids Res.
253389-3402. Query RECA_ECOLI "RecA protein
(Recombinase A)" (352 letters) Database
40scop1.59nm 3886 sequences 705,110
total letters Searching........done

Score E Sequences producing significant
alignments (bits)
Value 2reb-1 c.37.1.11 RECA PROTEIN
(E.C.3.4.99.37) 448
e-127 1g18A2 d.48.1.1 RECA PROTEIN
70 9e-14 1g0uF
d.153.1.4 PROTEASOME COMPONENT C1
32 0.020 1byrA d.136.1.1
ENDONUCLEASE
28 0.29 1g3qA c.37.1.10 CELL DIVISION
INHIBITOR 28
0.38 1ct5A c.1.6.2 YEAST HYPOTHETICAL PROTEIN,
SELENOMET 28 0.49 1g0uD
d.153.1.4 PROTEASOME COMPONENT PUP2
27 1.1 1e32A2 c.37.1.13 P97
26
1.4 1g0uA d.153.1.4 PROTEASOME COMPONENT Y7
26 1.9 1cp2A
c.37.1.10 NITROGENASE IRON PROTEIN
26 1.9 1f3oA c.37.1.12
HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN
25 2.4 1qj2B2 d.133.1.1 CARBON MONOXIDE
DEHYDROGENASE 25 3.2 1dgyA
c.72.1.1 ADENOSINE KINASE
25 3.2
51
BLASTP 2.2.1 Apr-13-2001 Reference Altschul,
Stephen F., Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb
Miller, and David J. Lipman (1997), "Gapped
BLAST and PSI-BLAST a new generation of protein
database search programs", Nucleic Acids Res.
253389-3402. Query RECA_ECOLI "RecA protein
(Recombinase A)" (352 letters) Database
40scop1.59nm 3886 sequences 705,110
total letters Searching........done

Score E Sequences producing significant
alignments (bits)
Value 2reb-1 c.37.1.11 RECA PROTEIN
(E.C.3.4.99.37) 448
e-127 1g18A2 d.48.1.1 RECA PROTEIN
70 9e-14 1g0uF
d.153.1.4 PROTEASOME COMPONENT C1
32 0.020 1byrA d.136.1.1
ENDONUCLEASE
28 0.29 1g3qA c.37.1.10 CELL DIVISION
INHIBITOR 28
0.38 1ct5A c.1.6.2 YEAST HYPOTHETICAL PROTEIN,
SELENOMET 28 0.49 1g0uD
d.153.1.4 PROTEASOME COMPONENT PUP2
27 1.1 1e32A2 c.37.1.13 P97
26
1.4 1g0uA d.153.1.4 PROTEASOME COMPONENT Y7
26 1.9 1cp2A
c.37.1.10 NITROGENASE IRON PROTEIN
26 1.9 1f3oA c.37.1.12
HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN
25 2.4 1qj2B2 d.133.1.1 CARBON MONOXIDE
DEHYDROGENASE 25 3.2 1dgyA
c.72.1.1 ADENOSINE KINASE
25 3.2 1skyB3 c.37.1.11
F1-ATPASE
25 3.2 1g6oA c.37.1.13 CAG-ALPHA
25 4.2 1cmxA
d.3.1.6 UBIQUITIN YUH1-UBAL
24 7.1 8abp- c.93.1.1
L-ARABINOSE-BINDING PROTEIN (MUTANT WITH MET
1... 24 7.1 2tpsA c.1.3.1 THIAMIN PHOSPHATE
SYNTHASE 24
7.1 1b8aA1 b.40.4.1 ASPARTYL-TRNA SYNTHETASE
24 7.1 1qtsA1
b.1.10.1 AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT
(ALPHA- 24 7.1 1b15A c.2.1.2 ALCOHOL
DEHYDROGENASE 23
9.3 1pmi- b.82.1.3 PHOSPHOMANNOSE ISOMERASE
23 9.3 gt2reb-1
c.37.1.11 RECA PROTEIN (E.C.3.4.99.37)
Length 243 Score 448 bits (1152), Expect
e-127 Identities 243/266 (91), Positives
243/266 (91), Gaps 23/266 (8) Query 3
DENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALG
AGGLPMGRIV 62 DENKQKALAAALGQIEKQFGKGSIM
RLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIV Sbjct 1
DENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALG
AGGLPMGRIV 60 Query 63 EIYGPESSGKTTLTLQVIAAAQRE
GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTG 122
EIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVD
IDNLLCSQPDTG Sbjct 61 EIYGPESSGKTTLTLQVIAAAQREGK
TCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTG 120 Query
123 EQALEICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAA
RMMSQAMRKLAGNL 182 EQALEICDALARSGAVDVIV
VDSVAALTPKAEIE GLAARMMSQAMRKLAGNL Sbjct
121 EQALEICDALARSGAVDVIVVDSVAALTPKAEIE--------GLAA
RMMSQAMRKLAGNL 172 Query 183 KQSNTLLIFINQIRMKIGV
MFGNPETTTGGNALKFYASVRLDIRRIGAVKEGENVVGSET 242
KQSNTLLIFINQ
TGGNALKFYASVRLDIRRIGAVKEGENVVGSET Sbjct 173
KQSNTLLIFINQ---------------TGGNALKFYASVRLDIRRIGAVK
EGENVVGSET 217 Query 243 RVKVVKNKIAAPFKQAEFQILYG
EGI 268 RVKVVKNKIAAPFKQAEFQILYGEGI Sbjc
t 218 RVKVVKNKIAAPFKQAEFQILYGEGI 243 gt1g18A2
d.48.1.1 RECA PROTEIN Length 60
Score 70.1 bits (170), Expect 9e-14
Identities 30/56 (53), Positives 44/56
(78) Query 272 GELVDLGVKEKLIEKAGAWYSYKGEKIGQGKA
NATAWLKDNPETAKEIEKKVRELL 327 G LDGV
LI KGAWYGEGQGK NA L N A EIEKKE
L Sbjct 4 GSLIDMGVDQGLIRKSGAWFTYEGEQLGQGKENARNF
LVENADVADEIEKKIKEKL 59 gt1g0uF d.153.1.4
PROTEASOME COMPONENT C1 Length 242
Score 32.3 bits (72), Expect 0.020
Identities 25/88 (28), Positives 47/88
(53), Gaps 9/88 (10) Query 271
YGELVDLGVKEKLIEKAGAWYSYKGEKIGQGKANATAWLK----DNPE--
TAKEIEKKVR 324 G G E G
YKG GG A A L PE AE K Sbjct 132
FGGVDKNGAHLYMLEPSGSYWGYKGAATGKGRQSAKAELEKLVDHHPEGL
SAREAVKQAA 191 Query 325 EL--LLSNPNSTPDFSVDDSE-G
VAETN 349 L N DF S
ETN Sbjct 192 KIIYLAHEDNKEKDFELEISWCSLSETN
219
Bit Score
Raw Score
52
Database 40scop1.59nm Posted date Jun
22, 2002 306 PM Number of letters in
database 705,110 Number of sequences in
database 3886 Lambda K H 0.314
0.134 0.369 Gapped Lambda K H
0.267 0.0410 0.140 Matrix BLOSUM62 Gap
Penalties Existence 11, Extension 1 Number of
Hits to DB 469,543 Number of Sequences
3886 Number of extensions 18494 Number of
successful extensions 65 Number of sequences
better than 10.0 17 Number of HSP's better than
10.0 without gapping 13 Number of HSP's
successfully gapped in prelim test 4 Number of
HSP's that attempted gapping in prelim test
50 Number of HSP's gapped (non-prelim) 17 length
of query 352 length of database
705,110 effective HSP length 79 effective length
of query 273 effective length of database
398,116 effective search space
108685668 effective search space used 108685668
53
??????????????
?????(Sequence Identity)()
100
0
10
20
30
40
70
50
60
80
90
25
15
5
35
?????30??
????
BLAST?E-value lt 0.0001
PSI-BLAST?E-value lt 0.0001
?????????
54
BLAST?????????
????? ???????? ???? ????????
blastn ?? ?? 2? ??????DB?????? ???DNA?????????cDNA????????????????????????
blastp ???? ???? 1? ???????????????????????
blastx ??(?????????) ???? 6? ?????6???????????????? ???DNA?????(???????????????)?????
tblastn ???? ??(?????????) 6? ?????6???????????????? ??????????????????????????
tblastn ??(?????????) ??(?????????) 36? ????DB??6???????????????? ?????????????????????????????????DB???????????????????
55
DNA?????????????3?????????????
AGCTTTTCATTCTGACTGCA TCGAAAAA
CAAGACTGACGT
DNA????????? ???????? A?T?G?C??????? ??????????? ?
????
AGCTTTTCATTCTGACTGCA S F S F x L Q A F H
S D C L F I L T A
3?????1??????? ???????????? ????????????? 3???????
?? ????????
???????????????????????????????
56
blastp(?????????)?????????????
???T.thermophius??????, ????????????????
BLASTP 2.2.3 May-13-2002 Query X07 AAS80531.1
tthe0 (144 letters) Database ecoli_aa
4237 sequences 1,350,094 total letters

Score E Sequences producing
significant alignments
(bits) Value infC NP_416233.1 "protein chain
initiation factor IF-3" NC_000913 137
2e-34 rhsD NP_415030.1 "RhsD protein in RhsD
element" NC_000913 28 0.19 pta
NP_416800.1 "phosphotransacetylase" NC_000913
25 2.0 prsA NP_415725.1
"phosphoribosylpyrophosphate synthetase"
NC_000913 25 2.7 yiaK NP_418032.1
"2,3-diketo-L-gulonate dehydrogenase,
NADH-depe... 24 3.5 ffh NP_417101.1
"4.5S-RNP protein, GTP-binding export factor,
pa... 24 4.6 ybdR NP_415141.1 "putative
dehydrogenase, NAD(P)-binding" NC_000913 24
4.6 ydfG NP_416057.1 "putative oxidoreductase"
NC_000913 23 7.8 gtinfC
NP_416233.1 "protein chain initiation factor
IF-3" NC_000913 Length 180 Score
137 bits (346), Expect 2e-34 Identities
72/139 (51), Positives 92/139 (65), Gaps
1/139 (0) Query 4 REALRLAQEMDLDLVLVGPNADPPVAR
IMDYSKWRYEQQMXXXXXXXXXXXTEVKSIKFR 63
REAL AE DLV PNAPPV RIMDY K YE
VK IKFR Sbjct 40 REALEKAEEAGVDLVEISPNAEPPVCRI
MDYGKFLYEKSKSSKEQKKKQKVIQVKEIKFR 99 Query 64
VKIDEHDYQTKLGHIKRFLQEGHKVKVTIMFRGREVAHPELGERILNRVT
EDLKDLAVVE 123 DE DYQ KL RFLEG
K KT FRGREAH G LNRV DLLAVVE Sbjct 100
PGTDEGDYQVKLRSLIRFLEEGDKAKITLRFRGREMAHQQIGMEVLNRVK
DDLQELAVVE 159 Query 124 MKPEML-GRDMNMLLAPVK
141 P GR M MLAP K Sbjct 160
SFPTKIEGRQMIMVLAPKK 178 gtrhsD NP_415030.1 "RhsD
protein in RhsD element" NC_000913
Length 1426 Score 28.5 bits (62), Expect
0.19 Identities 17/52 (32), Positives 25/52
(47) Query 80 RFLQEGHKVKVTIMFRGREVAHPELGERILNR
VTEDLKDLAVVEMKPEMLGR 131 RL E VT
REV H E G V L D V GR Sbjct 383
RYLYEQDRITVTDSLNRREVLHTEGGAGLKRVVKKELADGSVTRSGYDAA
GR 434
57
blastp(?????????)????)
ORF????????H.influenzae?ORF?????ORF
? HI0078?cysteine tRNA syntetase
? HI0083?????????????
58
????

• ??? ? ?????????????? (2001) ????
• ?????? ??????????????????????????? ???2?? (2007)
  ???
• Arthur M.Lesk(????????? ??)?????????????????
  ???????????????(2003), ???????????????????
• D.W.Mount??????????? ???????????????
  ???????????? -? ?2? ???????????????2005??11500?
• ????? ????????????????????????(2007) ????
• R.Durbin ?????????? ????????????? -
  ???????????????????2001??9800?
• BLAST WEB page http//www.ncbi.nlm.nih.gov/BLAST/