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= 045263
(742 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 226 bits (576), Expect = 3e-59, Method: Compositional matrix adjust.
Identities = 175/526 (33%), Positives = 260/526 (49%), Gaps = 81/526 (15%)
Query: 207 LDKCISCVPGLSKRLYHQLENCGFYTLRKLLHHFPRTYADLQNAQIDLDDGQYFIFIGEI 266
L I G+ +L+ G TLR LL FPR Y D + L+D + GE
Sbjct: 113 LSTDIQYAKGVGPNRKKKLKKLGIETLRDLLEFFPRDYEDRRKI-FKLND----LLPGEK 167
Query: 267 ISSRGMKAGCSFSFLEVIVGCEIADTETTSGDEVVNIDSGQKKKIYLHLK-KFFRGTRFT 325
++++G IV E T + +NI + +H+ K+F
Sbjct: 168 VTTQGK-----------IVSVE------TKKFQNMNILTAVLSDGLVHVPLKWFNQDYLQ 210
Query: 326 SIPFLKSIEGKHKVGEFVCVSGKVRAMRSNNHYEMREYNIDVLKDEDDLSLRAKGRPYPI 385
+ +LK + GK V V+G V++ YE+ +N +V E + R PI
Sbjct: 211 T--YLKQLTGKE-----VFVTGTVKSNAYTGQYEI--HNAEVTPKEGEYVRRI----LPI 257
Query: 386 YPSKGGLNASLLRDTIARALQALPANF-DPVPKEITQEFGLLCLFDAYMGIHQPKHIDEA 444
Y G++ +R + +L + + +P+ I ++ LL + DAY G+H PK
Sbjct: 258 YRLTSGISQKQMRKIFEENIPSLCCSLKETLPERILEKRKLLGVKDAYYGMHFPKTFYHL 317
Query: 445 DLARKRLIFDEFFYLQLGRLYQMLEGLGTQFEKEGLLDKYRKPRLNAAYMEGWSSLTKKL 504
+ AR+RL ++E F LQL + + + EK G + K +EG L ++
Sbjct: 318 EKARERLAYEELFVLQLA-----FQKIRKEREKHGGIPKK---------IEG--KLAEEF 361
Query: 505 LRALPYSLTSSQLSAISEIIWDLKQPVPMNRLLQGDVGCGKTVVAFLACMEVIGSGYQAA 564
+++LP+ LT++Q A EI D+ PMNRLLQGDVG GKTVVA LA ++ +G+Q A
Sbjct: 362 IKSLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTA 421
Query: 565 FMVPTELLATQHYEHLLKLLDNMEEDKHKPKIALLTGSTPVKQSRMIRKDLQTGDITLVI 624
FMVPT +LA QHY ++ K +ALL G+T + I+ L+ G I +VI
Sbjct: 422 FMVPTSILAIQHYRRTVESF-----SKFNIHVALLIGATTPSEKEKIKSGLRNGQIDVVI 476
Query: 625 GTHSLIAEKVEFSALRLAIVDEQQRFGVVQRGRFNSKLYYTSMSSGMAMVNSDGSPKDDQ 684
GTH+LI E V F L L I+DEQ RFGV QR M+ G MV++
Sbjct: 477 GTHALIQEDVHFKNLGLVIIDEQHRFGVKQREAL--------MNKG-KMVDT-------- 519
Query: 685 HMAPHVLAMSATPIPRTLALALYGDMSLTQITDLPPGRIPIKTYII 730
L MSATPIPR++ALA YGD+ +T I ++PPGR ++T ++
Sbjct: 520 ------LVMSATPIPRSMALAFYGDLDVTVIDEMPPGRKEVQTMLV 559
>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
Length = 1151
Score = 123 bits (309), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 76/225 (33%), Positives = 114/225 (50%), Gaps = 28/225 (12%)
Query: 507 ALPYSLTSSQLSAISEIIWDLKQPVPMNRLLQGDVGCGKTVVAFLACMEVIGSGYQAAFM 566
+ P+ T Q AI+ ++ D+ QP+ M+RL+ GDVG GKT VA A + + Q A +
Sbjct: 599 SFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVL 658
Query: 567 VPTELLATQHYEHLLKLLDNMEEDKHKPKIALLTGSTPVKQSRMIRKDLQTGDITLVIGT 626
VPT LLA QHY++ N +I +++ K+ I ++ G I ++IGT
Sbjct: 659 VPTTLLAQQHYDNFRDRFANW-----PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGT 713
Query: 627 HSLIAEKVEFSALRLAIVDEQQRFGVVQRGRFNSKLYYTSMSSGMAMVNSDGSPKDDQHM 686
H L+ V+F L L IVDE+ RFGV + R + N D
Sbjct: 714 HKLLQSDVKFKDLGLLIVDEEHRFGVRHKERIKA-----------MRANVD--------- 753
Query: 687 APHVLAMSATPIPRTLALALYGDMSLTQITDLPPGRIPIKTYIIE 731
+L ++ATPIPRTL +A+ G L+ I P R+ +KT++ E
Sbjct: 754 ---ILTLTATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVRE 795
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 32.7 bits (73), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 536 LLQGDVGCGKTV---VAFLACMEVIGSGYQAAFMVPTELLATQHYEHLLKLLDNMEEDKH 592
+ Q G GKT V+ L C+++ QA + PT LA Q + LL L D M H
Sbjct: 42 IAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQSH 101
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 32.7 bits (73), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 506 RALPYSLTSSQLSAISEIIWDLKQPVPMNRLLQGDVGCGKTVVAFLACMEVIGSGYQAAF 565
R P++L Q +AIS I D + V L+ GKTVVA A + + + + +
Sbjct: 179 RTYPFTLDPFQDTAISCI--DRGESV----LVSAHTSAGKTVVAEYAIAQSLKNKQRVIY 232
Query: 566 MVPTELLATQHYEHLL 581
P + L+ Q Y LL
Sbjct: 233 TSPIKALSNQKYRELL 248
>pdb|3P4Y|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
- P2 Form
Length = 415
Score = 32.7 bits (73), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 529 QPVPMNRLLQGD-------VGCGKTVVAFLACMEVIGSGYQAAFMVPTELLATQHYEHLL 581
Q + R++QG G GKT + + + G ++A + PT L Q E L
Sbjct: 27 QRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQ 86
Query: 582 KLLD 585
KL D
Sbjct: 87 KLAD 90
>pdb|3OIY|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3OIY|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 414
Score = 32.7 bits (73), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 529 QPVPMNRLLQGD-------VGCGKTVVAFLACMEVIGSGYQAAFMVPTELLATQHYEHLL 581
Q + R++QG G GKT + + + G ++A + PT L Q E L
Sbjct: 26 QRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQ 85
Query: 582 KLLD 585
KL D
Sbjct: 86 KLAD 89
>pdb|2XGJ|A Chain A, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
pdb|2XGJ|B Chain B, Structure Of Mtr4, A Dexh Helicase Involved In Nuclear Rna
Processing And Surveillance
Length = 1010
Score = 32.7 bits (73), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 6/76 (7%)
Query: 506 RALPYSLTSSQLSAISEIIWDLKQPVPMNRLLQGDVGCGKTVVAFLACMEVIGSGYQAAF 565
R P++L Q +AIS I D + V L+ GKTVVA A + + + + +
Sbjct: 81 RTYPFTLDPFQDTAISCI--DRGESV----LVSAHTSAGKTVVAEYAIAQSLKNKQRVIY 134
Query: 566 MVPTELLATQHYEHLL 581
P + L+ Q Y LL
Sbjct: 135 TSPIKALSNQKYRELL 150
>pdb|3P4X|A Chain A, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
pdb|3P4X|B Chain B, Helicase Domain Of Reverse Gyrase From Thermotoga Maritima
Length = 413
Score = 32.7 bits (73), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 529 QPVPMNRLLQGD-------VGCGKTVVAFLACMEVIGSGYQAAFMVPTELLATQHYEHLL 581
Q + R++QG G GKT + + + G ++A + PT L Q E L
Sbjct: 25 QRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQ 84
Query: 582 KLLD 585
KL D
Sbjct: 85 KLAD 88
>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain
pdb|1Q0U|B Chain B, Crystal Structure Of The Bstdead N-Terminal Domain
Length = 219
Score = 32.3 bits (72), Expect = 0.90, Method: Composition-based stats.
Identities = 35/117 (29%), Positives = 50/117 (42%), Gaps = 13/117 (11%)
Query: 538 QGDVGCGKTVVAFLACMEVIG---SGYQAAFMVPTELLATQHYEHLLKLLDNMEEDKHKP 594
Q G GKT L E I + QA PT LATQ Y LK+ +D+
Sbjct: 47 QSQTGTGKTHAYLLPIXEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRXIV 106
Query: 595 KIALLTGSTPVKQSRMIRKDLQTGDITLVIGTHSLIAEKVEFSAL-----RLAIVDE 646
L+ G+ KQ + + ++Q +VIGT I + + AL + +VDE
Sbjct: 107 ARCLIGGTD--KQKALEKLNVQP---HIVIGTPGRINDFIREQALDVHTAHILVVDE 158
>pdb|4DDT|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 2
pdb|4DDU|A Chain A, Thermotoga Maritima Reverse Gyrase, C2 Form 1
pdb|4DDV|A Chain A, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDV|B Chain B, Thermotoga Maritima Reverse Gyrase, Triclinic Form
pdb|4DDW|A Chain A, Thermotoga Maritima Reverse Gyrase, C-centered
Orthorhombic Form
pdb|4DDX|A Chain A, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
pdb|4DDX|B Chain B, Thermotoga Maritima Reverse Gyrase, Primitive Monoclinic
Form
Length = 1104
Score = 32.0 bits (71), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 529 QPVPMNRLLQGD-------VGCGKTVVAFLACMEVIGSGYQAAFMVPTELLATQHYEHLL 581
Q + R++QG G GKT + + + G ++A + PT L Q E L
Sbjct: 83 QRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQ 142
Query: 582 KLLDN 586
KL D
Sbjct: 143 KLADE 147
>pdb|2P6R|A Chain A, Crystal Structure Of Superfamily 2 Helicase Hel308 In
Complex With Unwound Dna
pdb|2P6U|A Chain A, Apo Structure Of The Hel308 Superfamily 2 Helicase
Length = 702
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 37/129 (28%), Positives = 55/129 (42%), Gaps = 20/129 (15%)
Query: 534 NRLLQGDVGCGKTVVAFLACMEVIGSGYQAAFMVPTELLATQHYEHLLKLLDNMEEDKHK 593
N LL GKT++A +A + G ++ ++VP LA + YE K
Sbjct: 42 NLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESF----------KKW 91
Query: 594 PKIALLTG-STPVKQSRMIRKDLQTGDITLVIGTH----SLIAEKVEF-SALRLAIVDEQ 647
KI L G ST +SR D GD +++ T SLI + + A+ +VDE
Sbjct: 92 EKIGLRIGISTGDYESR----DEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEI 147
Query: 648 QRFGVVQRG 656
+RG
Sbjct: 148 HLLDSEKRG 156
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 536 LLQGDVGCGKTV---VAFLACMEVIGSGYQAAFMVPTELLATQHYEHLLKLLDNMEEDKH 592
+ Q G GKT V+ L C+++ QA + PT LA Q + LL L D M H
Sbjct: 42 IAQSQSGTGKTATFSVSVLQCLDIQVRETQALILAPTRELAVQVQKGLLALGDYMNVQCH 101
>pdb|3ZYY|X Chain X, Reductive Activator For Corrinoid,Iron-Sulfur Protein
pdb|3ZYY|Y Chain Y, Reductive Activator For Corrinoid,Iron-Sulfur Protein
Length = 631
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 33/126 (26%), Positives = 56/126 (44%), Gaps = 11/126 (8%)
Query: 99 FKYG-RADKDAMDDFDISLACKRFPCITLGSTPPVGLYDETKAGGSEMKSLLADQSCEAV 157
K+G RA + A++ IS A + T+G PPVG+ GS + LLA+ +
Sbjct: 408 IKHGMRAMQGAIERVSISEAGLKVKYQTVGGIPPVGIC------GSGLIDLLANLKRAGI 461
Query: 158 V--SNPMDAELRVDRFGLSEAWPSLYPALPNESSTSSEVGSLPSEASIEPLLDKCISCVP 215
+ S +D + +R E A NES + ++ + +EA I+ L+ +
Sbjct: 462 IDRSGKIDRTVNKERIREGEDGLEFVLAWANESGNNKDI--VITEADIQNLIRAKAAIFA 519
Query: 216 GLSKRL 221
G+ L
Sbjct: 520 GVRTML 525
>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|B Chain B, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0S|A Chain A, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 410
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 536 LLQGDVGCGKTV---VAFLACMEVIGSGYQAAFMVPTELLATQHYEHLLKLLDNMEEDKH 592
+ Q G GKT ++ L C+++ QA + PT LA Q + LL L D M H
Sbjct: 78 IAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCH 137
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 536 LLQGDVGCGKTV---VAFLACMEVIGSGYQAAFMVPTELLATQHYEHLLKLLDNMEEDKH 592
+ Q G GKT ++ L C+++ QA + PT LA Q + LL L D M H
Sbjct: 79 IAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCH 138
>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|X Chain X, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 411
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 536 LLQGDVGCGKTV---VAFLACMEVIGSGYQAAFMVPTELLATQHYEHLLKLLDNMEEDKH 592
+ Q G GKT ++ L C+++ QA + PT LA Q + LL L D M H
Sbjct: 79 IAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCH 138
>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|B Chain B, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|C Chain C, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|D Chain D, Crystal Structure Of Human Apo-Eif4aiii
Length = 391
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 536 LLQGDVGCGKTV---VAFLACMEVIGSGYQAAFMVPTELLATQHYEHLLKLLDNMEEDKH 592
+ Q G GKT ++ L C+++ QA + PT LA Q + LL L D M H
Sbjct: 57 IAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCH 116
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
0.320 0.137 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,824,658
Number of Sequences: 62578
Number of extensions: 917769
Number of successful extensions: 2408
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 2394
Number of HSP's gapped (non-prelim): 19
length of query: 742
length of database: 14,973,337
effective HSP length: 106
effective length of query: 636
effective length of database: 8,340,069
effective search space: 5304283884
effective search space used: 5304283884
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)