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= 006319
(650 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 538 bits (1385), Expect = e-153, Method: Compositional matrix adjust.
Identities = 299/666 (44%), Positives = 428/666 (64%), Gaps = 34/666 (5%)
Query: 1 MAKLDLTEDDEKVNIETIFWSAMDMLSDDDKKLPQVSNILPLLKRGIGVHHSGLLPILKE 60
M+KLD DDEK + IF +A+ +L + D++LPQ+ +ILPLL+RGIG+HHSGLLPILKE
Sbjct: 461 MSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKE 520
Query: 61 VIEILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAG 120
VIEILFQEG +K LFATETFSIGLNMPAKTVVFT+VRK+DG +FRW+S GEYIQMSGRAG
Sbjct: 521 VIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAG 580
Query: 121 RRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSYNMLLNQIRCEEGSPENLL 180
RRG+D+RGI I+M+D+KMEP AK M+KG AD L+SAFHL YNM+LN +R E SPE +L
Sbjct: 581 RRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFML 640
Query: 181 RNSFYQFQADHAIPDLEKQAKVLEEERDSMVIEEEDSLKNYYNLLQQYKSLKKDVRDIVF 240
+SF+QFQ ++P +EK+ L+++ D + +E+E+++K Y+ + Q K ++DVR +V
Sbjct: 641 EHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVT 700
Query: 241 SPKYCLPFLQPGRFVCIECTRGDDNSPSFSTEDHQVTWGVVIEFEK------VKGVYEDD 294
P L FLQPGR V I G DN WG V++F K VY D
Sbjct: 701 HPANALSFLQPGRLVEI-SVNGKDN----------YGWGAVVDFAKRINKRNPSAVYTD- 748
Query: 295 ANKKPEDSNYTVNILTRCVVSKDGAG-----KKTLK--IVPLKESGEPLVVSVPIS--QI 345
+Y VN++ + TL I P +E + + +PI+ I
Sbjct: 749 ------HESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSI 802
Query: 346 IKLSSARLPMPKDLLPLQTRENMLKSTSEFLARNASGLP-LDPEANMGIRSSSYQKLVRR 404
+ + RL MPKD+ +E + KS E R G+P LDP NM I + KL+++
Sbjct: 803 KSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKK 862
Query: 405 IEALESLFDKHEISKSPLIEQKLKVLHMKQELTAKIKSIKRQMRSSTELAFKDELKARKR 464
I+ L + + ++ S +E+ K +L +K +KR++ S + D+L+ RKR
Sbjct: 863 IDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKR 922
Query: 465 VLRRLGYATSDDVVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQE 524
VLRRLG+ T +D++ELKG+VACEISS +EL LTELIFNG ++K E+ +LLSCF +QE
Sbjct: 923 VLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQE 982
Query: 525 KLQDASKPREELELLFTQLQDTARRVAKVQLECKVQIDVEGFVNSFRPDIMEAVYAWAKG 584
+ ++A + + EL +++ A ++AK+ + K+++ + +V SFR ++ME VY W +G
Sbjct: 983 RCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRG 1042
Query: 585 SKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAKSIGETELEAKFEEAVSKIKRDIVF 644
+ F +I ++T V+EGSLIR +RLEE++++L+ A +IG + L+ K E + I RDIV
Sbjct: 1043 ATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVS 1102
Query: 645 AASLYL 650
A SLYL
Sbjct: 1103 AGSLYL 1108
>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 = 537 bits (1384), Expect = e-153, Method: Compositional matrix adjust.
Identities = 299/666 (44%), Positives = 428/666 (64%), Gaps = 34/666 (5%)
Query: 1 MAKLDLTEDDEKVNIETIFWSAMDMLSDDDKKLPQVSNILPLLKRGIGVHHSGLLPILKE 60
M+KLD DDEK + IF +A+ +L + D++LPQ+ +ILPLL+RGIG+HHSGLLPILKE
Sbjct: 363 MSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKE 422
Query: 61 VIEILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAG 120
VIEILFQEG +K LFATETFSIGLNMPAKTVVFT+VRK+DG +FRW+S GEYIQMSGRAG
Sbjct: 423 VIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAG 482
Query: 121 RRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAFHLSYNMLLNQIRCEEGSPENLL 180
RRG+D+RGI I+M+D+KMEP AK M+KG AD L+SAFHL YNM+LN +R E SPE +L
Sbjct: 483 RRGLDDRGIVIMMIDEKMEPQVAKGMVKGQADRLDSAFHLGYNMILNLMRVEGISPEFML 542
Query: 181 RNSFYQFQADHAIPDLEKQAKVLEEERDSMVIEEEDSLKNYYNLLQQYKSLKKDVRDIVF 240
+SF+QFQ ++P +EK+ L+++ D + +E+E+++K Y+ + Q K ++DVR +V
Sbjct: 543 EHSFFQFQNVISVPVMEKKLAELKKDFDGIEVEDEENVKEYHEIEQAIKGYREDVRQVVT 602
Query: 241 SPKYCLPFLQPGRFVCIECTRGDDNSPSFSTEDHQVTWGVVIEFEK------VKGVYEDD 294
P L FLQPGR V I G DN WG V++F K VY D
Sbjct: 603 HPANALSFLQPGRLVEISVN-GKDN----------YGWGAVVDFAKRINKRNPSAVYTD- 650
Query: 295 ANKKPEDSNYTVNILTRCVVSKDGAG-----KKTLK--IVPLKESGEPLVVSVPIS--QI 345
+Y VN++ + TL I P +E + + +PI+ I
Sbjct: 651 ------HESYIVNVVVNTMYIDSPVNLLKPFNPTLPEGIRPAEEGEKSICAVIPITLDSI 704
Query: 346 IKLSSARLPMPKDLLPLQTRENMLKSTSEFLARNASGLP-LDPEANMGIRSSSYQKLVRR 404
+ + RL MPKD+ +E + KS E R G+P LDP NM I + KL+++
Sbjct: 705 KSIGNLRLYMPKDIRASGQKETVGKSLREVNRRFPDGIPVLDPVKNMKIEDEDFLKLMKK 764
Query: 405 IEALESLFDKHEISKSPLIEQKLKVLHMKQELTAKIKSIKRQMRSSTELAFKDELKARKR 464
I+ L + + ++ S +E+ K +L +K +KR++ S + D+L+ RKR
Sbjct: 765 IDVLNTKLSSNPLTNSMRLEELYGKYSRKHDLHEDMKQLKRKISESQAVIQLDDLRRRKR 824
Query: 465 VLRRLGYATSDDVVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQE 524
VLRRLG+ T +D++ELKG+VACEISS +EL LTELIFNG ++K E+ +LLSCF +QE
Sbjct: 825 VLRRLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSCFAFQE 884
Query: 525 KLQDASKPREELELLFTQLQDTARRVAKVQLECKVQIDVEGFVNSFRPDIMEAVYAWAKG 584
+ ++A + + EL +++ A ++AK+ + K+++ + +V SFR ++ME VY W +G
Sbjct: 885 RCKEAPRLKPELAEPLKAMREIAAKIAKIMKDSKIEVVEKDYVESFRHELMEVVYEWCRG 944
Query: 585 SKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAKSIGETELEAKFEEAVSKIKRDIVF 644
+ F +I ++T V+EGSLIR +RLEE++++L+ A +IG + L+ K E + I RDIV
Sbjct: 945 ATFTQICKMTDVYEGSLIRMFKRLEELVKELVDVANTIGNSSLKEKMEAVLKLIHRDIVS 1004
Query: 645 AASLYL 650
A SLYL
Sbjct: 1005 AGSLYL 1010
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 278 bits (710), Expect = 1e-74, Method: Compositional matrix adjust.
Identities = 215/675 (31%), Positives = 340/675 (50%), Gaps = 64/675 (9%)
Query: 4 LDLTEDDEKVNIETIFWSAMDMLSDDDKKLPQVSNILPLLKRGIGVHHSGLLPILKEVIE 63
++ + EK I ++ L +D+ LPQ+ LL+RGI VHH GLLPI+KE+IE
Sbjct: 359 INFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIE 418
Query: 64 ILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRG 123
ILF +G IK LFATETF++GLN+P +TV+F+++RK DG+ R ++ GE+ QM+GRAGRRG
Sbjct: 419 ILFSKGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRG 478
Query: 124 IDERGICILMV-DDKMEPSTAKMMLKGSADSLNSAFHLSYNMLLNQIRCEEGSPENLLRN 182
+D G I+M + + +T K + G L S F L+YNM+LN +R E E +++
Sbjct: 479 LDSTGTVIVMAYNSPLSIATFKEVTMGVPTRLQSQFRLTYNMILNLLRIEALRVEEMIKY 538
Query: 183 SFYQFQADHAIPDLEKQAKVLEEERDSMVIEE----EDSLKNYYNLLQQYKSLKKDV-RD 237
SF + + P+ EKQ KVL+EE ++ + ++ ++ + L+ YK ++ ++
Sbjct: 539 SFSENAKETLQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQE 598
Query: 238 IVFSPKYCLPFLQPGRFVCIECTRGDDNSPSFSTEDHQVTWGVVIEFEKVKGVYEDDANK 297
+V SP L L+ GR V +F + + G V + V
Sbjct: 599 MVKSPS-ILHILKEGRLV------------AFRDPNDCLKLGFVFKVSLKDAVCVIMTFT 645
Query: 298 KPED-SNYTVNILTRCVVSKDGAGKKTLKIVPLKESGEPLVVSVPISQIIKLSSARLPMP 356
KP N N L DG ++ P + + + VP++ I ++ + P
Sbjct: 646 KPYKLPNGEPNHLI-YFPKADGYRRRNF---PKFQKTDFYMEEVPVTAIEVITKRKFAAP 701
Query: 357 ------KDLLPLQ----TRENML--KSTSEFLARNASGLPLDPEANMGIRSSSYQKLVRR 404
KD+ L N+L K+ E + GL + +Q L+ R
Sbjct: 702 LGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKI------------HQILLDR 749
Query: 405 IEALESLFDKHEISKSPLIEQKLKVLHMKQELTAKIKSIKRQMRSSTELAFKDELKARKR 464
+ +F I K P + Q + + KI+ + M S L+ + + R
Sbjct: 750 TNIRDEIFKLKSI-KCPNLSQHIVPKFKAHVIKKKIEELYHLM-SDQNLSLLPDYEKRLA 807
Query: 465 VLRRLGYATSDDVVELKGKVACEISSAEELTLTELIFNGVLKDVKVEEMVSLLSCFVWQE 524
VL+ + + V LKG+VACEI+S EL LTELI + L + EE+V+LLS FV++
Sbjct: 808 VLKDTEFIDQNHNVLLKGRVACEINSGYELVLTELILDNFLGSFEPEEIVALLSVFVYEG 867
Query: 525 KLQDASKPREELELLFTQLQDTARRVAKV--QLECKVQI-------DVEGFVNSFRPDIM 575
K ++ EE ++ +L +R+ ++ ++ C D F++ R +M
Sbjct: 868 KTRE-----EEPPIVTPRLAKGKQRIEEIYKKMLCVFNTHQIPLTQDEAEFLDRKRFAMM 922
Query: 576 EAVYAWAKGSKFYEIMEITPVFEGSLIRAIRRLEEVLQQLILAAKSIGETELEAKFEEAV 635
VY WA+G F EIME++P EG+++R I L+E+ +++ A+ IG + L K A
Sbjct: 923 NVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKTASIIIGNSTLHMKMSRAQ 982
Query: 636 SKIKRDIVFAASLYL 650
IKRDIVFAASLYL
Sbjct: 983 ELIKRDIVFAASLYL 997
>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 = 87.8 bits (216), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 59/181 (32%), Positives = 98/181 (54%), Gaps = 15/181 (8%)
Query: 43 LKRGIGVHHSGLLPILKEVIEILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVRKFDGD 102
+++G HH+GLL + V+E F+ G IK + AT T + G+N+PA+ V+ ++ +FDG
Sbjct: 295 VRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFDGY 354
Query: 103 KFRWISSGEYIQMSGRAGRRGIDERGICILMVDDKMEPSTAKMMLKGSADSLNSAF---- 158
R I EY QM+GRAGR G+DERG I++V + K + G + + S
Sbjct: 355 SKR-IKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVKRYIFGEPERITSKLGVET 413
Query: 159 HLSYNMLLNQIRCEEGSP-----ENLLRNSFYQFQADHAIP-DLEKQAKVLEEERDSMVI 212
HL ++ L I C+ + E+ ++F+ Q + ++ +LE+ + LE MV+
Sbjct: 414 HLRFHSL--SIICDGYAKTLEELEDFFADTFFFKQNEISLSYELERVVRQLENW--GMVV 469
Query: 213 E 213
E
Sbjct: 470 E 470
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 79.3 bits (194), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 40/99 (40%), Positives = 63/99 (63%), Gaps = 3/99 (3%)
Query: 42 LLKRGIGVHHSGLLPILKEVIEILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVRKFD- 100
L+ +G+ HH+GL L+++IE F++ IK + AT T + G+N+PA+TV+ ++ +F+
Sbjct: 310 LISKGVAYHHAGLSKALRDLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNK 369
Query: 101 --GDKFRWISSGEYIQMSGRAGRRGIDERGICILMVDDK 137
+ I EY QMSGRAGR G D+ G I++V DK
Sbjct: 370 KIAGYYDEIPIMEYKQMSGRAGRPGFDQIGESIVVVRDK 408
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 70.5 bits (171), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 34/95 (35%), Positives = 55/95 (57%), Gaps = 2/95 (2%)
Query: 42 LLKRGIGVHHSGLLPILKEVIEILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVRKFDG 101
LL G +HH+G+ + + ++E LF + I+ L +T T + G+N+PA TV+ + +
Sbjct: 376 LLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSP 435
Query: 102 DKFRWISSG--EYIQMSGRAGRRGIDERGICILMV 134
+K RW G + +QM GRAGR D +G IL+
Sbjct: 436 EKGRWTELGALDILQMLGRAGRPQYDTKGEGILIT 470
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
Query: 43 LKRGIGVHHSGLLPILKEVIEILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVRKFDGD 102
L G+G H GL P+ + ++E LF G I+ + A+ + G+N+ A V+ + + ++G
Sbjct: 1212 LLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGK 1271
Query: 103 KFRWISSGEY--IQMSGRAGRRGIDERGICILM 133
++ Y +QM G A R D+ G C++M
Sbjct: 1272 IHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIM 1304
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 70.5 bits (171), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 34/95 (35%), Positives = 55/95 (57%), Gaps = 2/95 (2%)
Query: 42 LLKRGIGVHHSGLLPILKEVIEILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVRKFDG 101
LL G +HH+G+ + + ++E LF + I+ L +T T + G+N+PA TV+ + +
Sbjct: 376 LLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSP 435
Query: 102 DKFRWISSG--EYIQMSGRAGRRGIDERGICILMV 134
+K RW G + +QM GRAGR D +G IL+
Sbjct: 436 EKGRWTELGALDILQMLGRAGRPQYDTKGEGILIT 470
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/93 (30%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
Query: 43 LKRGIGVHHSGLLPILKEVIEILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVRKFDGD 102
L G+G H GL P+ + ++E LF G I+ + A+ + G+N+ A V+ + + ++G
Sbjct: 1212 LLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGK 1271
Query: 103 KFRWISSGEY--IQMSGRAGRRGIDERGICILM 133
++ Y +QM G A R D+ G C++M
Sbjct: 1272 IHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIM 1304
>pdb|2ZJ2|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 1
pdb|2ZJ5|A Chain A, Archaeal Dna Helicase Hjm Complexed With Adp In Form 1
pdb|2ZJ8|A Chain A, Archaeal Dna Helicase Hjm Apo State In Form 2
pdb|2ZJA|A Chain A, Archaeal Dna Helicase Hjm Complexed With Amppcp In Form 2
Length = 720
Score = 63.2 bits (152), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 39/120 (32%), Positives = 63/120 (52%), Gaps = 2/120 (1%)
Query: 22 AMDMLSDDDKKLPQVSNILPLLKRGIGVHHSGLLPILKEVIEILFQEGLIKCLFATETFS 81
A++ L+D ++ P + ++ G+ HH+GL + ++E F++G+IK + AT T S
Sbjct: 272 ALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLS 331
Query: 82 IGLNMPAKTVVFTNVRKFDGDKFRWISSGEYIQMSGRAGRRGIDE--RGICILMVDDKME 139
G+N PA V+ ++ ++ I E QM GRAGR DE GI + DD E
Sbjct: 332 AGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPRE 391
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 33.5 bits (75), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 43/86 (50%), Gaps = 12/86 (13%)
Query: 42 LLKRGI--GVHHSGLLPILKEVIEILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVR-K 98
L +GI +H+GL ++ ++ FQ ++ + AT F +G+N P NVR
Sbjct: 256 LQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKP-------NVRFV 308
Query: 99 FDGDKFRWISSGEYIQMSGRAGRRGI 124
D R I S Y Q +GRAGR G+
Sbjct: 309 VHFDIPRNIES--YYQETGRAGRDGL 332
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 33.1 bits (74), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 42/86 (48%), Gaps = 12/86 (13%)
Query: 42 LLKRGI--GVHHSGLLPILKEVIEILFQEGLIKCLFATETFSIGLNMPAKTVVFTNVR-K 98
L +GI +H+GL ++ ++ FQ ++ + AT F G+N P NVR
Sbjct: 256 LQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKP-------NVRFV 308
Query: 99 FDGDKFRWISSGEYIQMSGRAGRRGI 124
D R I S Y Q +GRAGR G+
Sbjct: 309 VHFDIPRNIES--YYQETGRAGRDGL 332
>pdb|2GHI|A Chain A, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
pdb|2GHI|B Chain B, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
pdb|2GHI|C Chain C, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
pdb|2GHI|D Chain D, Crystal Structure Of Plasmodium Yoelii Multidrug
Resistance Protein 2
Length = 260
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 268 SFSTEDHQVTWGVVIEFEKVKGVYEDDANKKPEDS-NYTVNILTRC-VVSKDGAGKKTL 324
SFS H+ +GV IEF V Y N + S N+ + T C +V G+GK T+
Sbjct: 4 SFSLTSHEKKFGVNIEFSDVNFSYPKQTNHRTLKSINFFIPSGTTCALVGHTGSGKSTI 62
>pdb|3RC8|A Chain A, Human Mitochondrial Helicase Suv3 In Complex With Short
Rna Fragment
Length = 677
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 72 KCLFATETFSIGLNMPAKTVVFTNVRKFD----GDK-FRWISSGEYIQMSGRAGR 121
K L AT+ +GLN+ + ++F ++ K G++ I++ + +Q++GRAGR
Sbjct: 374 KILVATDAIGMGLNLSIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGR 428
>pdb|1X18|E Chain E, Contact Sites Of Era Gtpase On The Thermus Thermophilus
30s Subunit
Length = 231
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 2/67 (2%)
Query: 381 SGLPLDPEANMGIRSSSYQKL--VRRIEALESLFDKHEISKSPLIEQKLKVLHMKQELTA 438
+G+P + +G ++++ + V R+E LE+LF EI + P EQ+L L Q+ +
Sbjct: 82 AGMPYVNQRWLGGMLTNFKTIQRVHRLEELEALFASPEIEERPKKEQRLHELERLQKYLS 141
Query: 439 KIKSIKR 445
+ +KR
Sbjct: 142 GFRLLKR 148
>pdb|1LPJ|A Chain A, Human Crbp Iv
Length = 133
Score = 30.8 bits (68), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 29/70 (41%)
Query: 189 ADHAIPDLEKQAKVLEEERDSMVIEEEDSLKNYYNLLQQYKSLKKDVRDIVFSPKYCLPF 248
A I L K KV+E+ DS I SL+NY+ + + +D R + L
Sbjct: 28 ATRKIAKLLKPQKVIEQNGDSFTIHTNSSLRNYFVKFKVGEEFDEDNRGLDNRKCKSLVI 87
Query: 249 LQPGRFVCIE 258
R CI+
Sbjct: 88 WDNDRLTCIQ 97
>pdb|3RC3|A Chain A, Human Mitochondrial Helicase Suv3
Length = 677
Score = 30.4 bits (67), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 5/55 (9%)
Query: 72 KCLFATETFSIGLNMPAKTVVFTNVRKFD----GDK-FRWISSGEYIQMSGRAGR 121
K L AT+ GLN+ + ++F ++ K G++ I++ + +Q++GRAGR
Sbjct: 374 KILVATDAIGXGLNLSIRRIIFYSLIKPSINEKGERELEPITTSQALQIAGRAGR 428
>pdb|1ZQ1|C Chain C, Structure Of Gatde Trna-Dependent Amidotransferase From
Pyrococcus Abyssi
pdb|1ZQ1|D Chain D, Structure Of Gatde Trna-Dependent Amidotransferase From
Pyrococcus Abyssi
Length = 633
Score = 30.0 bits (66), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 23/45 (51%)
Query: 457 DELKARKRVLRRLGYATSDDVVELKGKVACEISSAEELTLTELIF 501
D L+A K+V R LG D V +KG EI +EL + +I
Sbjct: 211 DALRATKKVKRGLGTIRQDLNVSIKGGARIEIKGVQELDMIPIII 255
>pdb|4ADZ|A Chain A, Crystal Structure Of The Apo Form Of A Copper-Sensitive
Operon Regulator (Csor) Protein From Streptomyces
Lividans
pdb|4ADZ|B Chain B, Crystal Structure Of The Apo Form Of A Copper-Sensitive
Operon Regulator (Csor) Protein From Streptomyces
Lividans
Length = 136
Score = 29.3 bits (64), Expect = 6.6, Method: Composition-based stats.
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 604 AIRRLEEVLQQLILAAKSIGETELEAKFEEAVSKIKR 640
A++ LEE L+ + A G TE++AK EEA I R
Sbjct: 96 ALQLLEEHLRHCVADAALKGGTEIDAKVEEATKAIGR 132
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
0.318 0.134 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,935,109
Number of Sequences: 62578
Number of extensions: 745372
Number of successful extensions: 2108
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2074
Number of HSP's gapped (non-prelim): 33
length of query: 650
length of database: 14,973,337
effective HSP length: 105
effective length of query: 545
effective length of database: 8,402,647
effective search space: 4579442615
effective search space used: 4579442615
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)