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Examples of Alignment Formats |
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The amino acid sequence of MJ0577 was used as a query against the E. coli entries of the nr database. The E value threshold was set to 0.01. Four sequences were returned as shown below. Results were aligned using a few of the various formatting options (pairwise; flat query-anchored without identities; flat query-anchored with identities) available. |
Score E
Sequences producing significant alignments: (bits) Value
gi|2507517|sp|P39177|UP12_ECOLI UNKNOWN PROTEIN FROM 2D-PAG... 55 6e-09
gi|2507516|sp|P37903|UP03_ECOLI UNKNOWN PROTEIN 2D_000B3L F... 41 1e-04
gi|7429293|pir||C64888 conserved hypothetical protein b1376... 41 1e-04
gi|2507514|sp|P03807|YDAA_ECOLI 35.6 KDA PROTEIN IN TPX-FNR... 38 0.002
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gi|4062229|dbj|BAA35246.1| (D90702) Unknown protein from 2D-page (spots pr25/lm16/2d_000lr3) .
[Escherichia coli]
Length = 142
Score = 55.4 bits (131), Expect = 6e-09
Identities = 44/157 (28%), Positives = 79/157 (50%), Gaps = 17/157 (10%)
Query: 4 MYKKILYPTDFSETAEIALKHVKAFKTLKAEEVI--LLHVIDEREIKKRDIFSLLLGVAG 61
MYK I+ P D E E++ K V+ + L ++ + LLHV+ S L +
Sbjct: 1 MYKTIIMPVDVFEM-ELSDKAVRHAEFLAQDDGVIHLLHVLPG---------SASLSLHR 50
Query: 62 LNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV 121
V FE L++ EA+ +++ + ++K + G +E+ ++AE+ G
Sbjct: 51 FAADVRRFEEHLQH----EAQERLQTMVSHFTIDPSRIKQHVRFGSVRDEVNELAEELGA 106
Query: 122 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
D++++GS ++ LLGS +VI+ +N PVLVV+
Sbjct: 107 DVVVIGSR-NPSISTHLLGSNASSVIRHANLPVLVVR 142
sp|P37903|UP03_ECOLI UNKNOWN PROTEIN 2D_000B3L FROM 2D-PAGE
dbj|BAA14980.1| (D90775) Unknown protein from 2D-PAGE (SPOT 2D_000B3L) (fragment).
[Escherichia coli]
Length = 144
Score = 41.0 bits (94), Expect = 1e-04
Identities = 43/157 (27%), Positives = 72/157 (45%), Gaps = 15/157 (9%)
Query: 4 MYKKILYPTDFS--ETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAG 61
M + IL P D S E + + HV+ + EV L VI + LG+A
Sbjct: 1 MNRTILVPIDISDSELTQRVISHVEEEAKIDDAEVHFLTVIPSLP------YYASLGLA- 53
Query: 62 LNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV 121
E + L EAK+++E I K+ + +V + G P + I+++A+
Sbjct: 54 -----YSAELPAMDDLKAEAKSQLEEIIKKFKLPTDRVHVHVEEGSPKDRILELAKKIPA 108
Query: 122 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
+II+ SH + ++ LLGS V++ + VLVV+
Sbjct: 109 HMIIIASH-RPDITTYLLGSNAAAVVRHAECSVLVVR 144
pir||C64888 conserved hypothetical protein b1376 - Escherichia coli
gb|AAC74458.1| (AE000234) putative filament protein [Escherichia coli]
Length = 168
Score = 41.0 bits (94), Expect = 1e-04
Identities = 43/157 (27%), Positives = 72/157 (45%), Gaps = 15/157 (9%)
Query: 4 MYKKILYPTDFS--ETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAG 61
M + IL P D S E + + HV+ + EV L VI + LG+A
Sbjct: 25 MNRTILVPIDISDSELTQRVISHVEEEAKIDDAEVHFLTVIPSLP------YYASLGLA- 77
Query: 62 LNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGV 121
E + L EAK+++E I K+ + +V + G P + I+++A+
Sbjct: 78 -----YSAELPAMDDLKAEAKSQLEEIIKKFKLPTDRVHVHVEEGSPKDRILELAKKIPA 132
Query: 122 DIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
+II+ SH + ++ LLGS V++ + VLVV+
Sbjct: 133 HMIIIASH-RPDITTYLLGSNAAAVVRHAECSVLVVR 168
gi|2507514|sp|P03807|YDAA_ECOLI 35.6 KDA PROTEIN IN TPX-FNR INTERGENIC REGION
gi|7429180|pir||QQECX membrane protein ydaA - Escherichia coli
gi|1742190|dbj|BAA14926.1| (D90771) ORF_ID:o261#5~similar to [SwissProt Accession Number
P44195] [Escherichia coli]
gi|1742201|dbj|BAA14936.1| (D90772) ORF_ID:o261#5~similar to [SwissProt Accession Number
P44195] [Escherichia coli]
gi|1787594|gb|AAC74415.1| (AE000231) orf, hypothetical protein [Escherichia coli]
Length = 316
Score = 37.5 bits (85), Expect = 0.002
Identities = 18/53 (33%), Positives = 29/53 (53%)
Query: 106 GIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
G+P E I +AE I+++G+ G+T + LG+ E VI +LV+K
Sbjct: 248 GLPEEVIPDLAEHLQAGIVVLGTVGRTGISAAFLGNTAEQVIDHLRCDLLVIK 300
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In the flat query-anchored with identities format, dots are used in place of residues in the database hits that are identical to the aligned residues in the query sequence. This format is useful for rapid inspection of aligned sequences for conserved residues. Dashes in the sequence represent gaps. |
blast_tmp 4 MYKKILYPTDFS--ETAEIALKHVKAFKTLKAEEVI--LLHVIDEREIKKRDIFSLLLGV 59
1778525 1 ...T.IM.V.VF--.M-.LSD.A.RHAEF.AQDDGVIH....LPG---------.AS.SL 48
1742248 1 .NRT..V.I.I.DS.LTQRVIS..EEEAKIDDA..H--F.T..PSLP------YYAS..L 52
1787640 25 .NRT..V.I.I.DS.LTQRVIS..EEEAKIDDA..H--F.T..PSLP------YYAS..L 76
blast_tmp 60 AGLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDE 119
1778525 49 HRFAAD.RR..EH.QH----..QERLQTMVSHFTIDPSRI.QHVRF.SVRD.VNEL..EL 104
1742248 53 .------YSA.LPAMDD.KA...SQL.E.I.KFKLPTDR.HVHVEE.S.KDR.LEL.KKI 106
1787640 77 .------YSA.LPAMDD.KA...SQL.E.I.KFKLPTDR.HVHVEE.S.KDR.LEL.KKI 130
7429180 248 .L.E.V.PDL..HL 261
blast_tmp 120 GVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
1778525 105 .A.VVVI..R-NPSISTH....NASS..RHA.L.....R 142
1742248 107 PAHM..IA..-RPDITTY....NAAA.VRHAECS....R 144
1787640 131 PAHM..IA..-RPDITTY....NAAA.VRHAECS....R 168
7429180 262 QAG.VVL.TV.R.GISAAF..NTA.Q..DHLRCDL..I. 300
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In the flat query-anchored without identities format, all residues (both identical and non-identical) in the datbase hits are represented below the appropriate residues of the query sequence. |
blast_tmp 4 MYKKILYPTDFS--ETAEIALKHVKAFKTLKAEEVI--LLHVIDEREIKKRDIFSLLLGV 59
1778525 1 MYKTIIMPVDVF--EM-ELSDKAVRHAEFLAQDDGVIHLLHVLPG---------SASLSL 48
1742248 1 MNRTILVPIDISDSELTQRVISHVEEEAKIDDAEVH--FLTVIPSLP------YYASLGL 52
7429293 25 MNRTILVPIDISDSELTQRVISHVEEEAKIDDAEVH--FLTVIPSLP------YYASLGL 76
blast_tmp 60 AGLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDE 119
1778525 49 HRFAADVRRFEEHLQH----EAQERLQTMVSHFTIDPSRIKQHVRFGSVRDEVNELAEEL 104
1742248 53 A------YSAELPAMDDLKAEAKSQLEEIIKKFKLPTDRVHVHVEEGSPKDRILELAKKI 106
7429293 77 A------YSAELPAMDDLKAEAKSQLEEIIKKFKLPTDRVHVHVEEGSPKDRILELAKKI 130
1742201 248 GLPEEVIPDLAEHL 261
blast_tmp 120 GVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVK 158
1778525 105 GADVVVIGSR-NPSISTHLLGSNASSVIRHANLPVLVVR 142
1742248 107 PAHMIIIASH-RPDITTYLLGSNAAAVVRHAECSVLVVR 144
7429293 131 PAHMIIIASH-RPDITTYLLGSNAAAVVRHAECSVLVVR 168
1742201 262 QAGIVVLGTVGRTGISAAFLGNTAEQVIDHLRCDLLVIK 300
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