BLASTP 2.2.26 [Sep-21-2011]
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. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 007818
(588 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G9K|A Chain A, Structure Of The Ndi1 Protein From Saccharomyces
Cerevisiae
pdb|4G9K|B Chain B, Structure Of The Ndi1 Protein From Saccharomyces
Cerevisiae
pdb|4GAP|A Chain A, Structure Of The Ndi1 Protein From Saccharomyces
Cerevisiae In Complex With Nad+
pdb|4GAP|B Chain B, Structure Of The Ndi1 Protein From Saccharomyces
Cerevisiae In Complex With Nad+
pdb|4GAV|A Chain A, Structure Of The Ndi1 Protein From Saccharomyces
Cerevisiae In Complex With Quinone
pdb|4GAV|B Chain B, Structure Of The Ndi1 Protein From Saccharomyces
Cerevisiae In Complex With Quinone
Length = 471
Score = 32.3 bits (72), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 282 AIIGGYVQAKRSKEALALFHEMQATGIKPDAVT-TVHCLSACSQLGALDDGIWIHR 336
+II V K+ ++E +AT I PD T T+ LSA SQL ++ + +H+
Sbjct: 64 SIIEPIVNFALKKKGNVTYYEAEATSINPDRNTVTIKSLSAVSQLYQPENHLGLHQ 119
>pdb|4G6G|A Chain A, Crystal Structure Of Ndh With Trt
pdb|4G6G|B Chain B, Crystal Structure Of Ndh With Trt
pdb|4G6H|A Chain A, Crystal Structure Of Ndh With Nadh
pdb|4G6H|B Chain B, Crystal Structure Of Ndh With Nadh
pdb|4G73|A Chain A, Crystal Structure Of Ndh With Nadh And Quinone
pdb|4G73|B Chain B, Crystal Structure Of Ndh With Nadh And Quinone
pdb|4G74|A Chain A, Crystal Structure Of Ndh With Quinone
pdb|4G74|B Chain B, Crystal Structure Of Ndh With Quinone
Length = 502
Score = 32.0 bits (71), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 282 AIIGGYVQAKRSKEALALFHEMQATGIKPDAVT-TVHCLSACSQLGALDDGIWIHR 336
+II V K+ ++E +AT I PD T T+ LSA SQL ++ + +H+
Sbjct: 95 SIIEPIVNFALKKKGNVTYYEAEATSINPDRNTVTIKSLSAVSQLYQPENHLGLHQ 150
>pdb|3S1L|A Chain A, Crystal Structure Of Apo-Form Furx
pdb|3S1L|B Chain B, Crystal Structure Of Apo-Form Furx
pdb|3S1L|C Chain C, Crystal Structure Of Apo-Form Furx
pdb|3S1L|D Chain D, Crystal Structure Of Apo-Form Furx
pdb|3S2E|A Chain A, Crystal Structure Of Furx Nadh Complex 1
pdb|3S2E|B Chain B, Crystal Structure Of Furx Nadh Complex 1
pdb|3S2E|C Chain C, Crystal Structure Of Furx Nadh Complex 1
pdb|3S2E|D Chain D, Crystal Structure Of Furx Nadh Complex 1
pdb|3S2E|E Chain E, Crystal Structure Of Furx Nadh Complex 1
pdb|3S2E|F Chain F, Crystal Structure Of Furx Nadh Complex 1
pdb|3S2E|G Chain G, Crystal Structure Of Furx Nadh Complex 1
pdb|3S2E|H Chain H, Crystal Structure Of Furx Nadh Complex 1
pdb|3S2F|A Chain A, Crystal Structure Of Furx Nadh:furfural
pdb|3S2F|B Chain B, Crystal Structure Of Furx Nadh:furfural
pdb|3S2F|C Chain C, Crystal Structure Of Furx Nadh:furfural
pdb|3S2F|D Chain D, Crystal Structure Of Furx Nadh:furfural
pdb|3S2F|E Chain E, Crystal Structure Of Furx Nadh:furfural
pdb|3S2F|F Chain F, Crystal Structure Of Furx Nadh:furfural
pdb|3S2F|G Chain G, Crystal Structure Of Furx Nadh:furfural
pdb|3S2F|H Chain H, Crystal Structure Of Furx Nadh:furfural
pdb|3S2G|A Chain A, Crystal Structure Of Furx Nadh+:furfuryl Alcohol I
pdb|3S2G|B Chain B, Crystal Structure Of Furx Nadh+:furfuryl Alcohol I
pdb|3S2G|C Chain C, Crystal Structure Of Furx Nadh+:furfuryl Alcohol I
pdb|3S2G|D Chain D, Crystal Structure Of Furx Nadh+:furfuryl Alcohol I
pdb|3S2G|E Chain E, Crystal Structure Of Furx Nadh+:furfuryl Alcohol I
pdb|3S2G|F Chain F, Crystal Structure Of Furx Nadh+:furfuryl Alcohol I
pdb|3S2G|G Chain G, Crystal Structure Of Furx Nadh+:furfuryl Alcohol I
pdb|3S2G|H Chain H, Crystal Structure Of Furx Nadh+:furfuryl Alcohol I
pdb|3S2I|A Chain A, Crystal Structure Of Furx Nadh+:furfuryl Alcohol Ii
pdb|3S2I|B Chain B, Crystal Structure Of Furx Nadh+:furfuryl Alcohol Ii
pdb|3S2I|C Chain C, Crystal Structure Of Furx Nadh+:furfuryl Alcohol Ii
pdb|3S2I|D Chain D, Crystal Structure Of Furx Nadh+:furfuryl Alcohol Ii
pdb|3S2I|E Chain E, Crystal Structure Of Furx Nadh+:furfuryl Alcohol Ii
pdb|3S2I|F Chain F, Crystal Structure Of Furx Nadh+:furfuryl Alcohol Ii
pdb|3S2I|G Chain G, Crystal Structure Of Furx Nadh+:furfuryl Alcohol Ii
pdb|3S2I|H Chain H, Crystal Structure Of Furx Nadh+:furfuryl Alcohol Ii
Length = 340
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 45/186 (24%), Positives = 73/186 (39%), Gaps = 22/186 (11%)
Query: 356 MYAKCGNIAKALQVFHEMPERNSLTYTAIIGGLALHGKALDAISYFSEMIGVGLMPDEIT 415
+Y+ CG LQ + + E+ T ++ GG +G+ + A + VGL+PD++
Sbjct: 90 LYSACGYCEHCLQGWETLCEKQQNTGYSVNGG---YGEYVVADPNY-----VGLLPDKVG 141
Query: 416 FLGILSACCHGGLVDEGRKYFAQMSSIFRLSPKLKHYSCMVDLLGRSGLLEEAEQLIRSM 475
F+ I C G V +G K + V + G GL A Q R+M
Sbjct: 142 FVEIAPILCAGVTVYKGLKVTDTRPGQW------------VVISGIGGLGHVAVQYARAM 189
Query: 476 PM--AADVVVWGALFFACRLHGNVSIGERAAMKLLELDPQDSGIYVLLANMYRDSNMWEE 533
+ AA + L A RL V++ R L + G + +L +
Sbjct: 190 GLRVAAVDIDDAKLNLARRLGAEVAVNARDTDPAAWLQKEIGGAHGVLVTAVSPKAFSQA 249
Query: 534 AGKVRK 539
G VR+
Sbjct: 250 IGMVRR 255
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 61/152 (40%), Gaps = 28/152 (18%)
Query: 82 YPLLFKVCASLGLRFLGYEIFGHV-LKLGFDVD----MYVHNAVIH------VFVSCGDL 130
+PL VCA+ F G ++ HV L L ++ M N ++ + V D+
Sbjct: 450 HPL---VCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDV 506
Query: 131 GLACNVFDESCVRNLVSWNSLINGFVRSGFPREAIRLFRDMQLE-------RVEPDEVTM 183
L CV N+ G V +G P+EA RL+R R+ E
Sbjct: 507 VLGLYYMTRDCV------NAKGEGMVLTG-PKEAERLYRSGLASLHARVKVRITEYEKDA 559
Query: 184 IGMVSACAQLEDLNLGREIHWYISESGLTLTV 215
G + A L+D +GR I W I GL ++
Sbjct: 560 NGELVAKTSLKDTTVGRAILWMIVPKGLPYSI 591
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 61/152 (40%), Gaps = 28/152 (18%)
Query: 82 YPLLFKVCASLGLRFLGYEIFGHV-LKLGFDVD----MYVHNAVIH------VFVSCGDL 130
+PL VCA+ F G ++ HV L L ++ M N ++ + V D+
Sbjct: 450 HPL---VCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDV 506
Query: 131 GLACNVFDESCVRNLVSWNSLINGFVRSGFPREAIRLFRDMQLE-------RVEPDEVTM 183
L CV N+ G V +G P+EA RL+R R+ E
Sbjct: 507 VLGLYYMTRDCV------NAKGEGMVLTG-PKEAERLYRSGLASLHARVKVRITEYEKDA 559
Query: 184 IGMVSACAQLEDLNLGREIHWYISESGLTLTV 215
G + A L+D +GR I W I GL ++
Sbjct: 560 NGELVAKTSLKDTTVGRAILWMIVPKGLPYSI 591
>pdb|1S4D|A Chain A, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|B Chain B, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|D Chain D, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|E Chain E, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|F Chain F, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|G Chain G, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|H Chain H, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|I Chain I, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|J Chain J, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|K Chain K, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|L Chain L, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
pdb|1S4D|M Chain M, Crystal Structure Analysis Of The S-adenosyl-l-methionine
Dependent Uroporphyrinogen-iii C-methyltransferase Sumt
Length = 280
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 356 MYAKCGNIAKALQVFHEMPERNSLTYTAIIGGLA------LHGKALDAISYFSEMIGVGL 409
++ + G A L V H++P R TA IGGLA H + A+++ + GL
Sbjct: 105 VFGRGGEEALTL-VEHQVPFRIVPGITAGIGGLAYAGIPVTHREVNHAVTFLTGHDSSGL 163
Query: 410 MPDEITFLGILSAC 423
+PD I + GI S
Sbjct: 164 VPDRINWQGIASGS 177
>pdb|3KE3|A Chain A, Crystal Structure Of Putative Serine-Pyruvate
Aminotransferase (Yp_263484.1) From Psychrobacter
Arcticum 273-4 At 2.20 A Resolution
Length = 379
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 523 NMYRDSNMWEEAGKVRKMMEERGVEKTPGCSSIEVNGLLYEFIVRDKSH 571
++ RD+ WE +VRK++ ++G+E E G++ + RD H
Sbjct: 274 DILRDAQ-WELGNRVRKVLTDKGIESV-AAEGFEAPGVVVSYTERDDXH 320
>pdb|4BBK|A Chain A, Structural And Functional Characterisation Of The
Kindlin-1 Pleckstrin Homology Domain
Length = 165
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 38/70 (54%), Gaps = 11/70 (15%)
Query: 160 FPREAIRLFRDMQLERVEPDEVTMIGMVSACAQLEDLNL-GREIHWYISESGLTLTVPLA 218
F +I F++ +LE+ EP E + C + D+N+ GR+ G+ L +P+A
Sbjct: 52 FKDTSIAYFKNKELEQGEPIEKLNL---RGCEIVPDVNVSGRKF-------GIKLLIPVA 101
Query: 219 NALMDMYVKC 228
+ + ++Y++C
Sbjct: 102 DGMNEVYLRC 111
>pdb|2NYS|A Chain A, X-Ray Crystal Structure Of Protein Agr_c_3712 From
Agrobacterium Tumefaciens. Northeast Structural Genomics
Consortium Target Atr88.
pdb|2NYS|B Chain B, X-Ray Crystal Structure Of Protein Agr_c_3712 From
Agrobacterium Tumefaciens. Northeast Structural Genomics
Consortium Target Atr88
Length = 176
Score = 30.4 bits (67), Expect = 2.8, Method: Composition-based stats.
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 269 FDDLPEKYVVPWNAIIGGY 287
F D PEK V+P+NAI G Y
Sbjct: 88 FSDTPEKLVIPYNAIRGFY 106
>pdb|2UZX|B Chain B, Structure Of The Human Receptor Tyrosine Kinase Met In
Complex With The Listeria Monocytogenes Invasion Protein
Inlb: Crystal Form I
pdb|2UZX|D Chain D, Structure Of The Human Receptor Tyrosine Kinase Met In
Complex With The Listeria Monocytogenes Invasion Protein
Inlb: Crystal Form I
pdb|2UZY|B Chain B, Structure Of The Human Receptor Tyrosine Kinase Met In
Complex With The Listeria Monocytogenes Invasion Protein
Inlb: Low Resolution, Crystal Form Ii
pdb|2UZY|D Chain D, Structure Of The Human Receptor Tyrosine Kinase Met In
Complex With The Listeria Monocytogenes Invasion Protein
Inlb: Low Resolution, Crystal Form Ii
Length = 727
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 322 CSQLGALDDGIWIHRFIEKENFNLNVVLGTALVDMYAKCGNIAKALQVFHEMPERNS 378
CS L G+W K+N N+ +V+ T D CG++ + H P ++
Sbjct: 80 CSSKANLSGGVW------KDNINMALVVDTYYDDQLISCGSVNRGTCQRHVFPHNHT 130
>pdb|1SHY|B Chain B, The Crystal Structure Of Hgf Beta-Chain In Complex With
The Sema Domain Of The Met Receptor
Length = 551
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 322 CSQLGALDDGIWIHRFIEKENFNLNVVLGTALVDMYAKCGNIAKALQVFHEMPERNS 378
CS L G+W K+N N+ +V+ T D CG++ + H P ++
Sbjct: 77 CSSKANLSGGVW------KDNINMALVVDTYYDDQLISCGSVNRGTCQRHVFPHNHT 127
>pdb|3OP5|A Chain A, Human Vaccinia-Related Kinase 1
pdb|3OP5|B Chain B, Human Vaccinia-Related Kinase 1
pdb|3OP5|C Chain C, Human Vaccinia-Related Kinase 1
pdb|3OP5|D Chain D, Human Vaccinia-Related Kinase 1
Length = 364
Score = 29.3 bits (64), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 52/99 (52%), Gaps = 4/99 (4%)
Query: 484 WGALFFACRLHGNVSIGERAAMKLLELDPQDSGIYVLLANMYRDSNMWEEAGK-VR-KMM 541
+G ++ A ++ + S+G A +++++P D+G Y+ + E+ K +R + +
Sbjct: 48 FGCIYLA-DMNSSESVGSDAPC-VVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKL 105
Query: 542 EERGVEKTPGCSSIEVNGLLYEFIVRDKSHPELEQIYDC 580
+ GV K G + NG Y F++ D+ +L++IY+
Sbjct: 106 KYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEA 144
>pdb|2KTY|A Chain A, Solution Structure Of Human Vaccinia Related Kinase-1
pdb|2KUL|A Chain A, Solution Structure Of Human Vaccinia Related Kinase
1(Vrk1)
Length = 368
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 52/99 (52%), Gaps = 4/99 (4%)
Query: 484 WGALFFACRLHGNVSIGERAAMKLLELDPQDSGIYVLLANMYRDSNMWEEAGK-VR-KMM 541
+G ++ A ++ + S+G A +++++P D+G Y+ + E+ K +R + +
Sbjct: 48 FGCIYLA-DMNSSESVGSDAPC-VVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKL 105
Query: 542 EERGVEKTPGCSSIEVNGLLYEFIVRDKSHPELEQIYDC 580
+ GV K G + NG Y F++ D+ +L++IY+
Sbjct: 106 KYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEA 144
>pdb|2LAV|A Chain A, Nmr Solution Structure Of Human Vaccinia-Related Kinase 1
Length = 361
Score = 28.9 bits (63), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 24/99 (24%), Positives = 52/99 (52%), Gaps = 4/99 (4%)
Query: 484 WGALFFACRLHGNVSIGERAAMKLLELDPQDSGIYVLLANMYRDSNMWEEAGK-VR-KMM 541
+G ++ A ++ + S+G A +++++P D+G Y+ + E+ K +R + +
Sbjct: 48 FGCIYLA-DMNSSESVGSDAPC-VVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKL 105
Query: 542 EERGVEKTPGCSSIEVNGLLYEFIVRDKSHPELEQIYDC 580
+ GV K G + NG Y F++ D+ +L++IY+
Sbjct: 106 KYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEA 144
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.324 0.140 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,207,693
Number of Sequences: 62578
Number of extensions: 713585
Number of successful extensions: 2134
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 2127
Number of HSP's gapped (non-prelim): 19
length of query: 588
length of database: 14,973,337
effective HSP length: 104
effective length of query: 484
effective length of database: 8,465,225
effective search space: 4097168900
effective search space used: 4097168900
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)