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= 001668
(1034 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 184 bits (467), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 142/501 (28%), Positives = 236/501 (47%), Gaps = 58/501 (11%)
Query: 16 VRFLAVSATIPNIEDIAEWLNV-PVQGIKRFGEEMRPVKL-------TTK---------- 57
VR + +SAT+PN ED+A +L V P +G+ F RPV L T K
Sbjct: 245 VRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMN 304
Query: 58 --VFDILMQYSRGKSALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKD-REQQERLREA 114
V++ +M+++ LVF +RK + A+ + + F+++ E LR
Sbjct: 305 EIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTE 364
Query: 115 SLSCSDKQMQSYILYGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHT 174
+ C + +++ + YG H+ G+ DR L+E LF +QVL +T TLA G+NLPAHT
Sbjct: 365 AEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHT 424
Query: 175 VVIKSTQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVIIMTRRETVHLYENLLNG 234
V+IK TQ ++ EKG + E ILQM GRAGRP ++ G I++T + Y +LLN
Sbjct: 425 VIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQ 484
Query: 235 CEMVESQLLSCVTEHLTAEIVQMTVSDITQAIEWMKCSYLYVRMKKNPQNYSVRK----- 289
+ESQ++S + + L AEIV V + A+ W+ +YLY+RM ++P Y +
Sbjct: 485 QLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKG 544
Query: 290 --VISRDRIE-KHMQEVCVQKVDELSCHQMIWTDEDGFLLKPQEPGRLMTKYYLKFDTMK 346
++ + R++ H + + K + ++ D+ + E GR+ + YY+ DT++
Sbjct: 545 DPLLDQRRLDLVHTAALMLDK------NNLVKYDKKTGNFQVTELGRIASHYYITNDTVQ 598
Query: 347 YIMQ--TPVNCGLEDALHTVCHAEEIAWIQLRRNEK----KLLNVINIDKDGRLRFHING 400
Q P +E + E I +R EK KLL + I
Sbjct: 599 TYNQLLKPTLSEIE-LFRVFSLSSEFKNITVREEEKLELQKLLERVPI------------ 645
Query: 401 DKGKRKKRIQTREEKIFVLANDCLIGDPSVHDLSLTQDMNSISTNGSRIAKCMRDYFIFR 460
K+ I+ KI VL I + +L DM ++ + R+ + + + + R
Sbjct: 646 ---PVKESIEEPSAKINVLLQ-AFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNR 701
Query: 461 KNYKGAVNSALLAKSLYQRLW 481
+ + L K + +R+W
Sbjct: 702 GWAQLTDKTLNLCKMIDKRMW 722
Score = 158 bits (400), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 137/528 (25%), Positives = 230/528 (43%), Gaps = 42/528 (7%)
Query: 16 VRFLAVSATIPNIEDIAEWLNVPVQGIKRFGEEMRPVKL-------------------TT 56
+R +A+S+++ N +D+A WL F +RPV L
Sbjct: 1084 IRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAK 1143
Query: 57 KVFDILMQYSRGKSALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKDREQQERLREASL 116
V+ + ++S K +VF +RK + A + T F+ E+ L
Sbjct: 1144 PVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKD--LIPYLE 1201
Query: 117 SCSDKQMQSYILYGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVV 176
SD ++ +L GVGY + GL +R L+E LF G +QV+ + +L G+N+ AH V+
Sbjct: 1202 KLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVI 1261
Query: 177 IKSTQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVIIMTRRETVHLYENLLNGCE 236
I TQY+N + Y+++ +LQM G A RP +D G +IM + ++ L
Sbjct: 1262 IMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPL 1321
Query: 237 MVESQLLSCVTEHLTAEIVQMTVSDITQAIEWMKCSYLYVRMKKNPQNYSVRKVISRDRI 296
VES L C+ +H AEIV T+ + A++++ ++LY RM +NP Y+++ IS +
Sbjct: 1322 PVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQG-ISHRHL 1380
Query: 297 EKHMQEVCVQKVDELSCHQMIWTDEDGFLLKPQEPGRLMTKYYLKFDTMK-YIMQTPVNC 355
H+ E+ Q + +L + I + ED + P G + YY+ + T++ + M
Sbjct: 1381 SDHLSELVEQTLSDLEQSKCI-SIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKT 1439
Query: 356 GLEDALHTVCHAEEIAWIQLRRNEKKLLNVINIDKDGRLRFHINGDKGKRKKRIQTREEK 415
+ + + +A E I +R +E LL + ++ +N K
Sbjct: 1440 KVRGLIEIISNAAEYENIPIRHHEDNLLRQLA----QKVPHKLNNPKFNDPH-------- 1487
Query: 416 IFVLANDCLIGDPSVHDLS--LTQDMNSISTNGSRIAKCMRDYFIFRKNYKGAVNSALLA 473
V N L S LS L D I + R+ + D A+ + LA
Sbjct: 1488 --VKTNLLLQAHLSRMQLSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELA 1545
Query: 474 KSLYQRLWDDSPYLLKQLPGIGMVTAKALHSMGIKS-FETLAEADPRR 520
+ + Q +W Y LKQLP K G++S F+ + D R
Sbjct: 1546 QMVTQAMWSKDSY-LKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEER 1592
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 182 bits (463), Expect = 6e-46, Method: Compositional matrix adjust.
Identities = 142/501 (28%), Positives = 235/501 (46%), Gaps = 58/501 (11%)
Query: 16 VRFLAVSATIPNIEDIAEWLNV-PVQGIKRFGEEMRPVKL-------TTK---------- 57
VR + +SAT+PN ED+A +L V P +G+ F RPV L T K
Sbjct: 245 VRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMN 304
Query: 58 --VFDILMQYSRGKSALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKD-REQQERLREA 114
V++ +M+++ LVF +RK + A+ + + F+++ E LR
Sbjct: 305 EIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTE 364
Query: 115 SLSCSDKQMQSYILYGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHT 174
+ C + +++ + YG H+ G+ DR L+E LF +QVL +T TLA G+NLPAHT
Sbjct: 365 AEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHT 424
Query: 175 VVIKSTQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVIIMTRRETVHLYENLLNG 234
V+IK TQ ++ EKG + E ILQM GRAGRP ++ G I++T + Y +LLN
Sbjct: 425 VIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQ 484
Query: 235 CEMVESQLLSCVTEHLTAEIVQMTVSDITQAIEWMKCSYLYVRMKKNPQNYSVRK----- 289
+ESQ++S + + L AEIV V + A+ W+ +YLY+RM ++P Y +
Sbjct: 485 QLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKG 544
Query: 290 --VISRDRIE-KHMQEVCVQKVDELSCHQMIWTDEDGFLLKPQEPGRLMTKYYLKFDTMK 346
++ + R++ H + + K + ++ D+ + E GR+ + YY+ DT++
Sbjct: 545 DPLLDQRRLDLVHTAALMLDK------NNLVKYDKKTGNFQVTELGRIASHYYITNDTVQ 598
Query: 347 YIMQ--TPVNCGLEDALHTVCHAEEIAWIQLRRNEK----KLLNVINIDKDGRLRFHING 400
Q P +E + E I +R EK KLL + I
Sbjct: 599 TYNQLLKPTLSEIE-LFRVFSLSSEFKNITVREEEKLELQKLLERVPI------------ 645
Query: 401 DKGKRKKRIQTREEKIFVLANDCLIGDPSVHDLSLTQDMNSISTNGSRIAKCMRDYFIFR 460
K+ I+ KI VL I + +L DM ++ R+ + + + + R
Sbjct: 646 ---PVKESIEEPSAKINVLLQ-AFISQLKLEGFALMADMVYVTQLAGRLMRAIFEIVLNR 701
Query: 461 KNYKGAVNSALLAKSLYQRLW 481
+ + L K + +R+W
Sbjct: 702 GWAQLTDKTLNLCKMIDKRMW 722
Score = 158 bits (400), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 137/528 (25%), Positives = 230/528 (43%), Gaps = 42/528 (7%)
Query: 16 VRFLAVSATIPNIEDIAEWLNVPVQGIKRFGEEMRPVKL-------------------TT 56
+R +A+S+++ N +D+A WL F +RPV L
Sbjct: 1084 IRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAK 1143
Query: 57 KVFDILMQYSRGKSALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKDREQQERLREASL 116
V+ + ++S K +VF +RK + A + T F+ E+ L
Sbjct: 1144 PVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKD--LIPYLE 1201
Query: 117 SCSDKQMQSYILYGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVV 176
SD ++ +L GVGY + GL +R L+E LF G +QV+ + +L G+N+ AH V+
Sbjct: 1202 KLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVI 1261
Query: 177 IKSTQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVIIMTRRETVHLYENLLNGCE 236
I TQY+N + Y+++ +LQM G A RP +D G +IM + ++ L
Sbjct: 1262 IMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPL 1321
Query: 237 MVESQLLSCVTEHLTAEIVQMTVSDITQAIEWMKCSYLYVRMKKNPQNYSVRKVISRDRI 296
VES L C+ +H AEIV T+ + A++++ ++LY RM +NP Y+++ IS +
Sbjct: 1322 PVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQG-ISHRHL 1380
Query: 297 EKHMQEVCVQKVDELSCHQMIWTDEDGFLLKPQEPGRLMTKYYLKFDTMK-YIMQTPVNC 355
H+ E+ Q + +L + I + ED + P G + YY+ + T++ + M
Sbjct: 1381 SDHLSELVEQTLSDLEQSKCI-SIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKT 1439
Query: 356 GLEDALHTVCHAEEIAWIQLRRNEKKLLNVINIDKDGRLRFHINGDKGKRKKRIQTREEK 415
+ + + +A E I +R +E LL + ++ +N K
Sbjct: 1440 KVRGLIEIISNAAEYENIPIRHHEDNLLRQLA----QKVPHKLNNPKFNDPH-------- 1487
Query: 416 IFVLANDCLIGDPSVHDLS--LTQDMNSISTNGSRIAKCMRDYFIFRKNYKGAVNSALLA 473
V N L S LS L D I + R+ + D A+ + LA
Sbjct: 1488 --VKTNLLLQAHLSRMQLSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELA 1545
Query: 474 KSLYQRLWDDSPYLLKQLPGIGMVTAKALHSMGIKS-FETLAEADPRR 520
+ + Q +W Y LKQLP K G++S F+ + D R
Sbjct: 1546 QMVTQAMWSKDSY-LKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEER 1592
>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 = 101 bits (252), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 67/228 (29%), Positives = 110/228 (48%), Gaps = 36/228 (15%)
Query: 15 SVRFLAVSATIPNIEDIAEWLNVPVQGIKRFGEEMRPVKL--------TTKVFDILMQYS 66
++R + +SAT PN+ +IAEWL+ + + RPV L T ++FD S
Sbjct: 172 ALRVIGLSATAPNVTEIAEWLDADY-----YVSDWRPVPLVEGVLCEGTLELFDGAFSTS 226
Query: 67 R--------------GKSALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKDREQQERLR 112
R LVF STR+GA++ A +LS Y +++ ++ +
Sbjct: 227 RRVKFEELVEECVAENGGVLVFESTRRGAEKTAVKLSAITAKY------VENEGLEKAIL 280
Query: 113 EASLSCSDKQMQSYILYGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPA 172
E + +++ + G +H+ GL R ++E F +G+++V+ T TLA G+NLPA
Sbjct: 281 EENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPA 340
Query: 173 HTVVIKSTQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVIIMT 220
V+++S F+ G S QM GRAGRP ++ G II+
Sbjct: 341 RRVIVRSLYRFD---GYSKRIKVSEYKQMAGRAGRPGMDERGEAIIIV 385
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 97.1 bits (240), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 89/280 (31%), Positives = 132/280 (47%), Gaps = 52/280 (18%)
Query: 6 PEMKSSSLASVR--FLAVSATIPNIEDIAEWLNVPVQGIKRFGEEMRPVKLTTKVF---- 59
P ++S ++ + R LA+SATI N + IA+WL G + RPV L V
Sbjct: 164 PVVESVTIRAKRRNLLALSATISNYKQIAKWL-----GAEPVATNWRPVPLIEGVIYPER 218
Query: 60 --------------------DILMQY-----SRGKSALVFCSTRKGAQEAAQQLSQTAMT 94
D ++ Y S+ LVF ++RK A+ A +++
Sbjct: 219 KKKEYNVIFKDNTTKKVHGDDAIIAYTLDSLSKNGQVLVFRNSRKMAESTALKIAN---- 274
Query: 95 YGYSNPFIKDR----EQQERLREASLSCSDKQ--MQSYILYGVGYHNGGLCLKDRNLIEG 148
Y N D E ++L + SD++ ++S I GV YH+ GL R+LIE
Sbjct: 275 --YMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEE 332
Query: 149 LFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQYFNKE-KGLYMEHDRSTILQMCGRAGR 207
F + ++V+ T TLA G+NLPA TV+I FNK+ G Y E QM GRAGR
Sbjct: 333 GFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMSGRAGR 392
Query: 208 PPFNDTGTVIIMTR-RETVH--LYENLLNGCEMVESQLLS 244
P F+ G I++ R +E V + +L+ E +ES+L S
Sbjct: 393 PGFDQIGESIVVVRDKEDVDRVFKKYVLSDVEPIESKLGS 432
>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 = 90.5 bits (223), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 69/232 (29%), Positives = 113/232 (48%), Gaps = 38/232 (16%)
Query: 13 LASVRFLAVSATIPNIEDIAEWLNVPVQGIKRFGEEMRPVKLTTKVF------------D 60
L + + +SATI N E++AEWLN + + RPVKL VF D
Sbjct: 167 LGKAQIIGLSATIGNPEELAEWLNAEL-----IVSDWRPVKLRRGVFYQGFVTWEDGSID 221
Query: 61 ILMQYS--------RGKSALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKD-REQQERL 111
+ + K AL+F + R+ A+ A +LS+ + + P I+ E + L
Sbjct: 222 RFSSWEELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSL-LTKPEIRALNELADSL 280
Query: 112 REASLSCSDKQMQSYILYGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLP 171
E + +++++ I GV +H+ GL +R L+E F KG ++ + T TL+ GIN P
Sbjct: 281 EE---NPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTP 337
Query: 172 AHTVVIKSTQYFNKEKGLYMEHDRSTIL---QMCGRAGRPPFNDTGTVIIMT 220
A V+I+ ++ +R I+ QM GRAGRP +++ G II++
Sbjct: 338 AFRVIIRDIWRYSD-----FGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVS 384
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 68.9 bits (167), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 56/178 (31%), Positives = 82/178 (46%), Gaps = 20/178 (11%)
Query: 55 TTKVFDILMQYSRGKSAL---VFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKDREQQERL 111
+ K + ++ Y R + L VF ++K +E A L K++ Q
Sbjct: 320 SKKTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNN------KEKSQIHMF 373
Query: 112 REASLSCSDKQ---------MQSYILYGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTN 162
E S++ K+ +S + G+ H+GGL + LIE LF KG ++VL T
Sbjct: 374 IEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATE 433
Query: 163 TLAHGINLPAHTVVIKSTQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVIIMT 220
T A G+NLP TV+ S + + GL E QM GRAGR + TGTVI+M
Sbjct: 434 TFAMGLNLPTRTVIFSSIRKHDG-NGL-RELTPGEFTQMAGRAGRRGLDSTGTVIVMA 489
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 65.1 bits (157), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 45/158 (28%), Positives = 79/158 (50%), Gaps = 17/158 (10%)
Query: 71 ALVFCSTRKGAQEAAQQLSQT---------AMTYGYSNPFIKDREQQERLREASLSCSDK 121
+VF +++ +E A ++S+ A+T ++N E L + K
Sbjct: 444 VIVFSFSKRDCEELALKMSKLDFNSDDEKEALTKIFNNAIALLPETDRELPQI------K 497
Query: 122 QMQSYILYGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQ 181
+ + G+G H+ GL + +IE LF +G ++VL T T + G+N+PA TVV S +
Sbjct: 498 HILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVR 557
Query: 182 YFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVIIM 219
++ ++ ++ +QM GRAGR +D G VI+M
Sbjct: 558 KWDGQQFRWVSG--GEYIQMSGRAGRRGLDDRGIVIMM 593
>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 = 65.1 bits (157), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 34/90 (37%), Positives = 54/90 (60%), Gaps = 2/90 (2%)
Query: 130 GVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQYFNKEKGL 189
G+G H+ GL + +IE LF +G ++VL T T + G+N+PA TVV S + ++ ++
Sbjct: 408 GIGIHHSGLLPILKEVIEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFR 467
Query: 190 YMEHDRSTILQMCGRAGRPPFNDTGTVIIM 219
++ +QM GRAGR +D G VI+M
Sbjct: 468 WVSG--GEYIQMSGRAGRRGLDDRGIVIMM 495
>pdb|3GV5|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna
And Incoming Ddadp
pdb|3GV5|D Chain D, Human Dna Polymerase Iota In Complex With T Template Dna
And Incoming Ddadp
Length = 420
Score = 38.9 bits (89), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTG-------RKYPFGNHIKESLL 540
+K++PGIG TAK L ++GI S L P+ +E G +K FG +L
Sbjct: 236 IKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVIL 295
Query: 541 SLPPK 545
S PP+
Sbjct: 296 SGPPQ 300
>pdb|3H40|A Chain A, Binary Complex Of Human Dna Polymerase Iota With Template
UT
Length = 389
Score = 38.9 bits (89), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTG-------RKYPFGNHIKESLL 540
+K++PGIG TAK L ++GI S L P+ +E G +K FG +L
Sbjct: 211 IKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVIL 270
Query: 541 SLPPK 545
S PP+
Sbjct: 271 SGPPQ 275
>pdb|1T3N|A Chain A, Structure Of The Catalytic Core Of Dna Polymerase Iota In
Complex With Dna And Dttp
pdb|1T3N|B Chain B, Structure Of The Catalytic Core Of Dna Polymerase Iota In
Complex With Dna And Dttp
pdb|1ZET|A Chain A, X-Ray Data Do Not Support Hoogsteen Base-Pairing During
Replication By Human Polymerase Iota
Length = 388
Score = 38.9 bits (89), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTG-------RKYPFGNHIKESLL 540
+K++PGIG TAK L ++GI S L P+ +E G +K FG +L
Sbjct: 210 IKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVIL 269
Query: 541 SLPPK 545
S PP+
Sbjct: 270 SGPPQ 274
>pdb|2DPI|A Chain A, Ternary Complex Of Hpoli With Dna And Dctp
pdb|2DPJ|A Chain A, Structure Of Hpoli With Dna And Dttp
pdb|2FLN|A Chain A, Binary Complex Of Catalytic Core Of Human Dna Polymerase
Iota With Dna (Template A)
pdb|2FLP|A Chain A, Binary Complex Of The Catalytic Core Of Human Dna
Polymerase Iota With Dna (Template G)
pdb|2FLL|A Chain A, Ternary Complex Of Human Dna Polymerase Iota With Dna And
Dttp
pdb|3EPG|A Chain A, Structure Of Human Dna Polymerase Iota Complexed With
N2-Ethylguanine
pdb|3EPI|A Chain A, Structure Of Human Dna Polymerase Iota Complexed With
N2-Ethylguanine And Incoming Ttp
pdb|3G6V|A Chain A, Dna Synthesis Across An Abasic Lesion By Human Dna
Polymerase-Iota
pdb|3G6X|A Chain A, Ternary Complex Of Dna Polymerase Iota:dna:dgtp With An
Abasic Site At The Templating Position
pdb|3G6Y|A Chain A, Ternary Complex Of Dna Polymerase Iota:dna:dttp With An
Abasic Site At The Templating Position
pdb|3GV7|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna
And Incoming Dttp
pdb|3GV8|B Chain B, Human Dna Polymerase Iota In Complex With T Template Dna
And Incoming Dgtp
pdb|3NGD|A Chain A, Structural Basis For Proficient Incorporation Of Dttp
Opposite O6- Methylguanine By Human Dna Polymerase Iota
pdb|3OSN|A Chain A, Structural Basis For Proficient Incorporation Of Dttp
Opposite O6- Methylguanine By Human Dna Polymerase Iota
pdb|3Q8P|B Chain B, Human Dna Polymerase Iota Incorporating Dctp Opposite
8-Oxo-Guanine
pdb|3Q8Q|B Chain B, Human Dna Polymerase Iota Incorporating Datp Opposite
8-Oxo-Guanine
pdb|3Q8R|B Chain B, Human Dna Polymerase Iota Incorporating Dgtp Opposite
8-Oxo-Guanine
pdb|3Q8S|B Chain B, Human Dna Polymerase Iota Incorporating Dttp Opposite
8-Oxo-Guanine
pdb|4EBC|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4EBD|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4EBE|A Chain A, Conformationally Restrained
North-Methanocarba-2'-Deoxyadenosine Corrects The
Error-Prone Nature Of Human Dna Polymerase Iota
pdb|4FS1|A Chain A, Base Pairing Mechanism Of N2,3-Ethenoguanine With Dttp By
Human Polymerase Iota
pdb|4FS2|A Chain A, Base Pairing Mechanism Of N2,3-Ethenoguanine With Dctp By
Human Polymerase Iota
pdb|4EYH|B Chain B, Human Dna Polymerase Iota Incorporating Dctp Opposite N-
(deoxyguanosin-8-yl)-1-aminopyrene Lesion
pdb|4EYI|B Chain B, Human Dna Polymerase Iota Incorporating Datp Opposite N-
(deoxyguanosin-8-yl)-1-aminopyrene Lesion
Length = 420
Score = 38.9 bits (89), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTG-------RKYPFGNHIKESLL 540
+K++PGIG TAK L ++GI S L P+ +E G +K FG +L
Sbjct: 236 IKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVIL 295
Query: 541 SLPPK 545
S PP+
Sbjct: 296 SGPPQ 300
>pdb|2ALZ|A Chain A, Ternary Complex Of Hpoli With Dna And Dctp
pdb|3H4B|A Chain A, Ternary Complex Of Human Dna Polymerase Iota With Template
UT AND Incoming Datp
pdb|3H4D|A Chain A, Ternary Complex Of Human Dna Polymerase Iota With Template
UT AND Incoming Dgtp
Length = 390
Score = 38.9 bits (89), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 33/65 (50%), Gaps = 7/65 (10%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTG-------RKYPFGNHIKESLL 540
+K++PGIG TAK L ++GI S L P+ +E G +K FG +L
Sbjct: 212 IKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVIL 271
Query: 541 SLPPK 545
S PP+
Sbjct: 272 SGPPQ 276
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 38.5 bits (88), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 14/99 (14%)
Query: 127 ILYG--------VGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIK 178
+LYG V +G L ++R+ + F +G +VL TTN LA GI++P ++V+
Sbjct: 258 VLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVN 317
Query: 179 STQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVI 217
++ + D +T + GR GR F G I
Sbjct: 318 ----YDLPTLANGQADPATYIHRIGRTGR--FGRKGVAI 350
>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3
pdb|3RRM|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Nup159, Gle1 H337r, Ip6
And Adp
pdb|3RRN|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Gle1 H337r And Ip6
Length = 395
Score = 38.5 bits (88), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 14/99 (14%)
Query: 127 ILYG--------VGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIK 178
+LYG V +G L ++R+ + F +G +VL TTN LA GI++P ++V+
Sbjct: 258 VLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVN 317
Query: 179 STQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVI 217
++ + D +T + GR GR F G I
Sbjct: 318 ----YDLPTLANGQADPATYIHRIGRTGR--FGRKGVAI 350
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 37.0 bits (84), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 37/150 (24%), Positives = 55/150 (36%), Gaps = 42/150 (28%)
Query: 71 ALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKDREQQERLREASLSCSDKQMQSYILYG 130
A++FC TRK A A +LS+ +
Sbjct: 285 AMIFCHTRKTASWLAAELSKEG------------------------------------HQ 308
Query: 131 VGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQYFNKEKGLY 190
V +G + ++ R + F +G +VL TTN A GI++ +VVI +K+
Sbjct: 309 VALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGN-- 366
Query: 191 MEHDRSTILQMCGRAGRPPFNDTGTVIIMT 220
D T L GR GR F G + M
Sbjct: 367 --PDNETYLHRIGRTGR--FGKRGLAVNMV 392
>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
pdb|3FMP|D Chain D, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 479
Score = 37.0 bits (84), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 37/150 (24%), Positives = 55/150 (36%), Gaps = 42/150 (28%)
Query: 71 ALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKDREQQERLREASLSCSDKQMQSYILYG 130
A++FC TRK A A +LS+ +
Sbjct: 336 AMIFCHTRKTASWLAAELSKEG------------------------------------HQ 359
Query: 131 VGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQYFNKEKGLY 190
V +G + ++ R + F +G +VL TTN A GI++ +VVI +K+
Sbjct: 360 VALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGN-- 417
Query: 191 MEHDRSTILQMCGRAGRPPFNDTGTVIIMT 220
D T L GR GR F G + M
Sbjct: 418 --PDNETYLHRIGRTGR--FGKRGLAVNMV 443
>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And
Rna
pdb|3FHT|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Amppnp And
Rna
Length = 412
Score = 37.0 bits (84), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 37/150 (24%), Positives = 55/150 (36%), Gaps = 42/150 (28%)
Query: 71 ALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKDREQQERLREASLSCSDKQMQSYILYG 130
A++FC TRK A A +LS+ +
Sbjct: 269 AMIFCHTRKTASWLAAELSKEG------------------------------------HQ 292
Query: 131 VGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQYFNKEKGLY 190
V +G + ++ R + F +G +VL TTN A GI++ +VVI +K+
Sbjct: 293 VALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGN-- 350
Query: 191 MEHDRSTILQMCGRAGRPPFNDTGTVIIMT 220
D T L GR GR F G + M
Sbjct: 351 --PDNETYLHRIGRTGR--FGKRGLAVNMV 376
>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
pdb|3EWS|B Chain B, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp
Length = 445
Score = 37.0 bits (84), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 37/150 (24%), Positives = 55/150 (36%), Gaps = 42/150 (28%)
Query: 71 ALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKDREQQERLREASLSCSDKQMQSYILYG 130
A++FC TRK A A +LS+ +
Sbjct: 306 AMIFCHTRKTASWLAAELSKEG------------------------------------HQ 329
Query: 131 VGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQYFNKEKGLY 190
V +G + ++ R + F +G +VL TTN A GI++ +VVI +K+
Sbjct: 330 VALLSGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGN-- 387
Query: 191 MEHDRSTILQMCGRAGRPPFNDTGTVIIMT 220
D T L GR GR F G + M
Sbjct: 388 --PDNETYLHRIGRTGR--FGKRGLAVNMV 413
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 36.2 bits (82), Expect = 0.100, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 14/99 (14%)
Query: 127 ILYG--------VGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIK 178
+LYG V +G L ++R+ + F +G +VL TTN LA GI++P ++V+
Sbjct: 50 VLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVN 109
Query: 179 STQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVI 217
++ + D +T + GR GR F G I
Sbjct: 110 ----YDLPTLANGQADPATYIHRIGRTGR--FGRKGVAI 142
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 34.7 bits (78), Expect = 0.29, Method: Composition-based stats.
Identities = 29/99 (29%), Positives = 46/99 (46%), Gaps = 14/99 (14%)
Query: 127 ILYG--------VGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIK 178
+LYG V +G L ++R+ + F +G +VL TTN LA GI++P + V+
Sbjct: 52 VLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVN 111
Query: 179 STQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVI 217
++ + D +T + GR GR F G I
Sbjct: 112 ----YDLPTLANGQADPATYIHRIGRTGR--FGRKGVAI 144
>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
H337r And Ip6
pdb|3PEV|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
And Ip6
Length = 188
Score = 34.7 bits (78), Expect = 0.29, Method: Composition-based stats.
Identities = 29/99 (29%), Positives = 46/99 (46%), Gaps = 14/99 (14%)
Query: 127 ILYG--------VGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIK 178
+LYG V +G L ++R+ + F +G +VL TTN LA GI++P + V+
Sbjct: 51 VLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVN 110
Query: 179 STQYFNKEKGLYMEHDRSTILQMCGRAGRPPFNDTGTVI 217
++ + D +T + GR GR F G I
Sbjct: 111 ----YDLPTLANGQADPATYIHRIGRTGR--FGRKGVAI 143
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 34.3 bits (77), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 48/199 (24%), Positives = 76/199 (38%), Gaps = 55/199 (27%)
Query: 18 FLAVSATIPNI--EDIAEWL--NVPVQGIKRFGEEMRPVKLTTKV--FDILMQY---SRG 68
F+A++AT + +DI L N P+ I F L K D LM+Y RG
Sbjct: 177 FMALTATADDTTRQDIVRLLGLNDPLIQISSFDRPNIRYMLMEKFKPLDQLMRYVQEQRG 236
Query: 69 KSALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKDREQQERLREASLSCSDKQMQSYIL 128
KS +++C++R ++ A +L QS +
Sbjct: 237 KSGIIYCNSRAKVEDTAARL-----------------------------------QSKGI 261
Query: 129 YGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQYFNKEKG 188
YH GL R ++ F + D+Q++ T GIN P V+ +F+ +
Sbjct: 262 SAAAYH-AGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVV----HFDIPRN 316
Query: 189 LYMEHDRSTILQMCGRAGR 207
+ + Q GRAGR
Sbjct: 317 I------ESYYQETGRAGR 329
>pdb|4G56|A Chain A, Crystal Structure Of Full Length Prmt5/mep50 Complexes
From Xenopus Laevis
pdb|4G56|C Chain C, Crystal Structure Of Full Length Prmt5/mep50 Complexes
From Xenopus Laevis
Length = 657
Score = 33.1 bits (74), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 45/91 (49%), Gaps = 8/91 (8%)
Query: 547 DMKIEEIKCQGQGKSKLLITLTRLSQSVQSTKRHYADMIVGAEEN-NMVLFHEKIRVDEF 605
+ I+ + G G+ L+ R ++ + + YA E+N N V+ E R +E+
Sbjct: 375 ETNIQILXVLGAGRGPLVNASLRAAKQAERKIKVYA-----VEKNPNAVITLEGWRYEEW 429
Query: 606 SSPYSVTVLSSNPQQGKLTVKADLIFEEYIG 636
S VTV+S + ++ K KAD+I E +G
Sbjct: 430 GS--QVTVVSGDXREWKAPEKADIIVSELLG 458
>pdb|2RB4|A Chain A, Crystal Structure Of The Helicase Domain Of Human Ddx25
Rna Helicase
pdb|2RB4|B Chain B, Crystal Structure Of The Helicase Domain Of Human Ddx25
Rna Helicase
Length = 175
Score = 32.7 bits (73), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 135 NGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQYFNKEKGLYMEHD 194
+G L ++ R I F G +VL TTN A GI++ T+V+ F+ E D
Sbjct: 65 SGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVN----FDLPVKQGEEPD 120
Query: 195 RSTILQMCGRAGR 207
T L GR GR
Sbjct: 121 YETYLHRIGRTGR 133
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%)
Query: 129 YGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQYFNKEKG 188
+ V +G + K+R++I F G +VL TT+ LA GI++ ++VI N+E
Sbjct: 305 FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 364
Query: 189 LY 190
++
Sbjct: 365 IH 366
>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|C Chain C, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|D Chain D, Crystal Structure Of The Eif4a-Pdcd4 Complex
pdb|2ZU6|F Chain F, Crystal Structure Of The Eif4a-Pdcd4 Complex
Length = 388
Score = 32.3 bits (72), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%)
Query: 129 YGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVIKSTQYFNKEKG 188
+ V +G + K+R++I F G +VL TT+ LA GI++ ++VI N+E
Sbjct: 279 FTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENY 338
Query: 189 LY 190
++
Sbjct: 339 IH 340
>pdb|2ZRU|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn
pdb|2ZRU|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn
pdb|2ZRU|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn
pdb|2ZRU|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn
pdb|2ZRV|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn.
pdb|2ZRV|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn.
pdb|2ZRV|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn.
pdb|2ZRV|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn.
pdb|2ZRW|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn And Ipp.
pdb|2ZRW|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn And Ipp.
pdb|2ZRW|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn And Ipp.
pdb|2ZRW|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn And Ipp.
pdb|2ZRX|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn And Dmapp.
pdb|2ZRX|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn And Dmapp.
pdb|2ZRX|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn And Dmapp.
pdb|2ZRX|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Fmn And Dmapp.
pdb|2ZRY|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Ipp.
pdb|2ZRY|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Ipp.
pdb|2ZRY|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Ipp.
pdb|2ZRY|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Ipp.
pdb|2ZRZ|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Dmapp
pdb|2ZRZ|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Dmapp
pdb|2ZRZ|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Dmapp
pdb|2ZRZ|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Dmapp
pdb|3B03|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Vipp.
pdb|3B03|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Vipp.
pdb|3B03|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Vipp.
pdb|3B03|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Vipp.
pdb|3B04|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Oipp.
pdb|3B04|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Oipp.
pdb|3B04|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Oipp.
pdb|3B04|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Oipp.
pdb|3B05|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Ipp At 2.2a Resolution.
pdb|3B05|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Ipp At 2.2a Resolution.
pdb|3B05|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Ipp At 2.2a Resolution.
pdb|3B05|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Ipp At 2.2a Resolution.
pdb|3B06|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Dmapp.
pdb|3B06|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Dmapp.
pdb|3B06|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Dmapp.
pdb|3B06|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase In Complex With Reduced Fmn And
Dmapp.
pdb|3VKJ|A Chain A, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase, Octameric Form
pdb|3VKJ|B Chain B, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase, Octameric Form
pdb|3VKJ|C Chain C, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase, Octameric Form
pdb|3VKJ|D Chain D, Crystal Structure Of Sulfolobus Shibatae Isopentenyl
Diphosphate Isomerase, Octameric Form
Length = 368
Score = 31.6 bits (70), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 24/46 (52%)
Query: 493 GIGMVTAKALHSMGIKSFETLAEADPRRIEIVTGRKYPFGNHIKES 538
GI M TAK L+S GIK+F+T + I I R GN ES
Sbjct: 198 GISMETAKLLYSYGIKNFDTSGQGGTNWIAIEMIRDIRRGNWKAES 243
>pdb|3EAQ|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAQ|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase Hera
Form 2, Complete Dimer, Symmetric
pdb|3EAR|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAR|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Partial Dimer
pdb|3EAS|A Chain A, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
pdb|3EAS|B Chain B, Novel Dimerization Motif In The Dead Box Rna Helicase
Hera: Form 1, Complete Dimer, Asymmetric
Length = 212
Score = 31.2 bits (69), Expect = 2.9, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 26/43 (60%)
Query: 135 NGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVI 177
+G L +R + G F +G+V+VL T+ A G+++P +V+
Sbjct: 62 HGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVV 104
>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSO|B Chain B, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|A Chain A, Crystal Structure Of A Translation Initiation Complex
pdb|2VSX|B Chain B, Crystal Structure Of A Translation Initiation Complex
Length = 395
Score = 31.2 bits (69), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 44/193 (22%), Positives = 77/193 (39%), Gaps = 57/193 (29%)
Query: 15 SVRFLAVSATIPN--IEDIAEWLNVPV-----------QGIKRF----GEEMRPVKLTTK 57
+ + + +SAT+PN +E +++ PV +GIK+F EE + T
Sbjct: 194 TTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEGIKQFYVNVEEEEYKYECLTD 253
Query: 58 VFDILMQYSRGKSALVFCSTRKGAQEAAQQLSQTAMTYGYSNPFIKDREQQERLREASLS 117
++D + A++FC+TR+ +E +L T + D QQER
Sbjct: 254 LYDSI----SVTQAVIFCNTRRKVEELTTKLRNDKFTV---SAIYSDLPQQER------- 299
Query: 118 CSDKQMQSYILYGVGYHNGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVI 177
D M+ F G ++L +T+ LA GI++ ++VI
Sbjct: 300 --DTIMKE------------------------FRSGSSRILISTDLLARGIDVQQVSLVI 333
Query: 178 KSTQYFNKEKGLY 190
NKE ++
Sbjct: 334 NYDLPANKENYIH 346
>pdb|1ZYB|A Chain A, Crystal Structure Of Transcription Regulator From
Bacteroides Thetaiotaomicron Vpi-5482 At 2.15 A
Resolution
Length = 232
Score = 31.2 bits (69), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 456 YFIFRKNYKGAVNSALLAKSLYQRLWDDSPYLLK 489
Y IFR NY V++ A++LY RLWD+ LK
Sbjct: 134 YDIFRLNYXNIVSNR--AQNLYSRLWDEPTLDLK 165
>pdb|3I32|A Chain A, Dimeric Structure Of A Hera Helicase Fragment Including
The C-Terminal Reca Domain, The Dimerization Domain, And
The Rna Binding Domain
Length = 300
Score = 30.8 bits (68), Expect = 3.8, Method: Composition-based stats.
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 135 NGGLCLKDRNLIEGLFLKGDVQVLCTTNTLAHGINLPAHTVVI 177
+G + +R + G F +G+V+VL T+ A G+++P +V+
Sbjct: 59 HGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVV 101
>pdb|1K1Q|A Chain A, Crystal Structure Of A Dinb Family Error Prone Dna
Polymerase From Sulfolobus Solfataricus
pdb|1K1Q|B Chain B, Crystal Structure Of A Dinb Family Error Prone Dna
Polymerase From Sulfolobus Solfataricus
pdb|1K1S|A Chain A, Crystal Structure Of Dinb From Sulfolobus Solfataricus
Length = 354
Score = 30.8 bits (68), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTGR 527
+ ++PGIG V A+ L+ +GI+ + + +E +TG+
Sbjct: 181 IDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGK 220
>pdb|3BQ0|A Chain A, Pre-insertion Binary Complex Of Dbh Dna Polymerase
pdb|3BQ1|A Chain A, Insertion Ternary Complex Of Dbh Dna Polymerase
pdb|3BQ2|A Chain A, Post-Insertion Binary Complex Of Dbh Dna Polymerase
pdb|4HYK|A Chain A, Dbh Ternary Complex (substrates Partially Disordered)
Length = 354
Score = 30.8 bits (68), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTGR 527
+ ++PGIG V A+ L+ +GI+ + + +E +TG+
Sbjct: 181 IDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGK 220
>pdb|4F4Y|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dbh
pdb|4F4Y|B Chain B, Y-family Dna Polymerase Chimera Dbh-dpo4-dbh
Length = 362
Score = 30.8 bits (68), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTGR 527
+ ++PGIG V A+ L+ +GI+ + + +E +TG+
Sbjct: 181 IDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGK 220
>pdb|1PZN|A Chain A, Rad51 (Rada)
pdb|1PZN|B Chain B, Rad51 (Rada)
pdb|1PZN|C Chain C, Rad51 (Rada)
pdb|1PZN|D Chain D, Rad51 (Rada)
pdb|1PZN|E Chain E, Rad51 (Rada)
pdb|1PZN|F Chain F, Rad51 (Rada)
pdb|1PZN|G Chain G, Rad51 (Rada)
Length = 349
Score = 30.8 bits (68), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTG 526
++ LPG+G TA+ L G + E +A A P ++ V G
Sbjct: 37 IEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAG 75
>pdb|4F50|A Chain A, Y-family Dna Polymerase Chimera Dbh-dbh-dpo4
Length = 361
Score = 30.4 bits (67), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTGR 527
+ ++PGIG V A+ L+ +GI+ + + +E +TG+
Sbjct: 181 IDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGK 220
>pdb|4F4W|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #1
pdb|4F4W|B Chain B, Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #1
pdb|4F4X|A Chain A, Y-family Dna Polymerase Chimera Dbh-dpo4-dpo4 #2
Length = 361
Score = 30.4 bits (67), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 488 LKQLPGIGMVTAKALHSMGIKSFETLAEADPRRIEIVTGR 527
+ ++PGIG V A+ L+ +GI+ + + +E +TG+
Sbjct: 181 IDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGK 220
>pdb|2WNW|A Chain A, The Crystal Structure Of Srfj From Salmonella Typhimurium
pdb|2WNW|B Chain B, The Crystal Structure Of Srfj From Salmonella Typhimurium
Length = 447
Score = 30.4 bits (67), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 28/119 (23%), Positives = 53/119 (44%), Gaps = 7/119 (5%)
Query: 513 LAEADPRRIEIVTGRKYPFGNHIKE--SLLSLPPKVDMKIEEIKCQGQGKSKLLITLTRL 570
L +DP R + + R F + ++ L+S+ P+ ++ + G G S
Sbjct: 5 LISSDPYRQQFLVERAVSFSHRQRDCSELISVLPRHALQ----QIDGFGGSFTEGAGVVF 60
Query: 571 SQSVQSTKRHYADMIVGAEENNMVLFHEKIRVDEFS-SPYSVTVLSSNPQQGKLTVKAD 628
+ + TK + + A+E+N L I+ +FS Y+ S++ QQG+L+ D
Sbjct: 61 NSMSEKTKAQFLSLYFSAQEHNYTLARMPIQSCDFSLGNYAYVDSSADLQQGRLSFSRD 119
>pdb|4GQB|A Chain A, Crystal Structure Of The Human Prmt5:mep50 Complex
Length = 637
Score = 30.0 bits (66), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 44/91 (48%), Gaps = 8/91 (8%)
Query: 547 DMKIEEIKCQGQGKSKLLITLTRLSQSVQSTKRHYADMIVGAEEN-NMVLFHEKIRVDEF 605
D ++ + G G+ L+ R ++ + YA E+N N V+ E + +E+
Sbjct: 355 DTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYA-----VEKNPNAVVTLENWQFEEW 409
Query: 606 SSPYSVTVLSSNPQQGKLTVKADLIFEEYIG 636
S VTV+SS+ ++ KAD+I E +G
Sbjct: 410 GS--QVTVVSSDMREWVAPEKADIIVSELLG 438
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
0.317 0.132 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,820,480
Number of Sequences: 62578
Number of extensions: 1163562
Number of successful extensions: 2609
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 2546
Number of HSP's gapped (non-prelim): 59
length of query: 1034
length of database: 14,973,337
effective HSP length: 109
effective length of query: 925
effective length of database: 8,152,335
effective search space: 7540909875
effective search space used: 7540909875
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: 56 (26.2 bits)