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= psy15878
(693 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 189 bits (480), Expect = 5e-48, Method: Compositional matrix adjust.
Identities = 173/649 (26%), Positives = 296/649 (45%), Gaps = 81/649 (12%)
Query: 1 MVHEKYQSLAKAAEEFKFYLEEYAGVK-----GQYPPTKRQLNKKSIYICTIEKGSKLIG 55
+ EKY+S K E G++ G Y L I + T EK LI
Sbjct: 80 LAGEKYESFKKW---------EKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIR 130
Query: 56 SLIQENRIDEIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINAL 115
+ + + I + +V+DE H+L+ +RG LE +V+K+ + K++++ +SAT N+ +
Sbjct: 131 N--RASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPNVTEI 188
Query: 116 STFIEGITYVENSRPTKHSEYVTVDKRVFQSFDGKSLTEIYADNLDYSLTGSGPDAVLHL 175
+ +++ YV + RP E V + + FDG T S + V
Sbjct: 189 AEWLDADYYVSDWRPVPLVEGVLCEG-TLELFDGAFST---------SRRVKFEELVEEC 238
Query: 176 VQGNLMVLIFCSSKIACSNLALRLQFDRFPGTKEYKKQEKEDLIEALKEENDGKLSTNLE 235
V N VL+F S++ A++L T +Y E E L +A+ EEN+G++S L
Sbjct: 239 VAENGGVLVFESTRRGAEKTAVKLS----AITAKY--VENEGLEKAILEENEGEMSRKLA 292
Query: 236 ECILYGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIR-----D 290
EC+ G A+HHA L G+RR++E+A+ G ++++ T TLAAGVNLPA+RVI+R D
Sbjct: 293 ECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIKVVVATPTLAAGVNLPARRVIVRSLYRFD 352
Query: 291 SYVGRDFISLNMYKQMVGRAGRTGLQESGESIMLCKTMQDFLRFSSMMNAGPEPISSHMD 350
Y R I ++ YKQM GRAGR G+ E GE+I++ + + PE I+S +
Sbjct: 353 GYSKR--IKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIAVKRYIFGEPERITSKLG 410
Query: 351 PPTLVDL-ILEVVAANLCSSLEDVKTLIKHTLFYQLKSPEDQQTFLETTLS---EIVASL 406
T + L ++ +LE+++ T F++ E +LS E V
Sbjct: 411 VETHLRFHSLSIICDGYAKTLEELEDFFADTFFFKQN---------EISLSYELERVVRQ 461
Query: 407 LASKGTMLTMNEAGHLSLTSIAKAAVQAGLSHDVCLIIYSDLLHNKLNFCLLNSLHMLFL 466
L + G ++ EA HL+ T + + V + I+ D+L +++ + +LH++
Sbjct: 462 LENWGMVV---EAAHLAPTKLG-SLVSRLYIDPLTGFIFHDVL-SRMELSDIGALHLIC- 515
Query: 467 VIPLEYRIPSDGILLSRSKVYDRYTKFHPQTLRVAEALGVTENLVALNVTGKLKDEKKAL 526
R P + R V + + R+ + L + ++ L + K A
Sbjct: 516 ------RTPD----MERLTVRKTDSWVEEEAFRLRKELSYYPSDFSVEYDWFLSEVKTA- 564
Query: 527 LCRFFHACILYDVLNFDNHQKVAKMYGIQNSHLQNFLNVTSYFASKVYRFCEELPELWCY 586
LC L D + + ++ YGI L+ + + ++ + R EE+
Sbjct: 565 LC-------LKDWIEEKDEDEICAKYGIAPGDLRRIVETAEWLSNAMNRIAEEVG----- 612
Query: 587 KQLLTDLPQTLMYCRAPNLRALMDLPGVKIGRARQLLNAGYSSLELIAR 635
++ L + + + L L+ + + RAR+L NAG + E I R
Sbjct: 613 NTSVSGLTERIKHGVKEELLELVRIRHIGRVRARKLYNAGIRNAEDIVR 661
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 138 bits (348), Expect = 9e-33, Method: Compositional matrix adjust.
Identities = 111/343 (32%), Positives = 160/343 (46%), Gaps = 35/343 (10%)
Query: 24 AGVKGQYPPTKRQLNKKSIYICTIEKGSKLIGSLIQENRIDEIGLIVIDEFHMLNEPQRG 83
A G Y L I I T EK L + ++E+ V+DE H LN+P+RG
Sbjct: 106 AMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRH--RPEWLNEVNYFVLDELHYLNDPERG 163
Query: 84 PILECVVSKVLYLKKSIQIFAMSATIGNINALSTFIEGITYVENSRPTKHSEYVTVDKRV 143
P++E V + K + A+SATI N ++ ++ N RP E V +R
Sbjct: 164 PVVESVTIRA----KRRNLLALSATISNYKQIAKWLGAEPVATNWRPVPLIEGVIYPERK 219
Query: 144 FQSFDGKSLTEIYADNLDYSLTGSGPDAV----LHLVQGNLMVLIFCSSKIACSNLALRL 199
+ ++ I+ DN + G DA+ L + N VL+F +S+ + AL++
Sbjct: 220 KKEYN-----VIFKDNTTKKVHGD--DAIIAYTLDSLSKNGQVLVFRNSRKMAESTALKI 272
Query: 200 QFDRFPGTKEYKKQEKEDLIEALK-----EENDGKLSTNLEECILYGVAYHHADLTAGER 254
+ ++ L E LK EE L+ I GVAYHHA L+ R
Sbjct: 273 A-----NYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALR 327
Query: 255 RLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGR-------DFISLNMYKQMV 307
LIEE + +++I T TLAAGVNLPA+ VII D Y D I + YKQM
Sbjct: 328 DLIEEGFRQRKIKVIVATPTLAAGVNLPARTVIIGDIYRFNKKIAGYYDEIPIMEYKQMS 387
Query: 308 GRAGRTGLQESGESIMLCKTMQDFLR-FSSMMNAGPEPISSHM 349
GRAGR G + GESI++ + +D R F + + EPI S +
Sbjct: 388 GRAGRPGFDQIGESIVVVRDKEDVDRVFKKYVLSDVEPIESKL 430
>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 = 125 bits (314), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 109/371 (29%), Positives = 169/371 (45%), Gaps = 38/371 (10%)
Query: 28 GQYPPTKRQLNKKSIYICTIEKGSKLI--GSLIQENRIDEIGLIVIDEFHMLNEPQRGPI 85
G Y L K I I T EK L+ GS + I ++ ++V DE H++ RG
Sbjct: 103 GDYDSKDEWLGKYDIIIATAEKFDSLLRHGS----SWIKDVKILVADEIHLIGSRDRGAT 158
Query: 86 LECVVSKVLYLKKSIQIFAMSATIGNINALSTFIEGITYVENSRPTKHSEYVTVDKRVFQ 145
LE +++ +L QI +SATIGN L+ ++ V + RP K V +Q
Sbjct: 159 LEVILAHML---GKAQIIGLSATIGNPEELAEWLNAELIVSDWRPVKLRRGV-----FYQ 210
Query: 146 SFDGKSLTEIYADNLDYSLTGSGPDAVLHLVQGNLMVLIFCSSKIACSNLALRLQFDRFP 205
F + ++ S + V ++ LIF + + +AL L
Sbjct: 211 GF-------VTWEDGSIDRFSSWEELVYDAIRKKKGALIFVNMRRKAERVALEL------ 257
Query: 206 GTKEYKKQEKEDLIEALKEENDG----KLSTNLEECILYGVAYHHADLTAGERRLIEEAY 261
+K+ K + I AL E D + L + I GVA+HHA L ER L+EE +
Sbjct: 258 -SKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENF 316
Query: 262 LAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDF----ISLNMYKQMVGRAGRTGLQE 317
G ++ + T TL+AG+N PA RVIIRD + DF I + QM+GRAGR E
Sbjct: 317 RKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDE 376
Query: 318 SGESIMLCKTMQDFLRFSSMMNAGPEPISSHM-DPPTLVDLILEVVAANLCSSLEDVKTL 376
GE I++ + + + PE + S + + L +L ++A S++E++
Sbjct: 377 VGEGIIVSTSDDPREVMNHYIFGKPEKLFSQLSNESNLRSQVLALIATFGYSTVEEILKF 436
Query: 377 IKHTLF-YQLK 386
I +T + YQ K
Sbjct: 437 ISNTFYAYQRK 447
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 105 bits (263), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 104/388 (26%), Positives = 191/388 (49%), Gaps = 44/388 (11%)
Query: 24 AGVKGQYPPTKRQLNKKSIYICTIEKGSKLIGSLIQENRIDEIGLIVIDEFHMLNEPQRG 83
A + G + K +++ I +CT EK + + + LI++DE H+L++ RG
Sbjct: 166 AELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-DRG 224
Query: 84 PILECVVSKVL----YLKKSIQIFAMSATIGNINALSTFI-----EGITYVENS-RPTK- 132
P+LE +V++ + ++ +++ +SAT+ N ++TF+ +G+ Y +NS RP
Sbjct: 225 PVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPL 284
Query: 133 HSEYVTV-DKRVFQSFDGKSLTEIYADNLDYSLTGSGPDAVLHLVQGNLMVLIFCSSKIA 191
YV + +K+ + F + + EI + + + H + ++V + +
Sbjct: 285 EQTYVGITEKKAIKRF--QIMNEIVYEKI-----------MEHAGKNQVLVFVHSRKETG 331
Query: 192 CSNLALR---LQFDRFPGTKEYKKQEKEDLIEALKEENDGKLSTNLEECILYGVAYHHAD 248
+ A+R L+ D T +E E L+ E + + L++ + YG A HHA
Sbjct: 332 KTARAIRDMCLEKD----TLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAG 387
Query: 249 LTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYV-----GR--DFISLN 301
+T +R L+E+ + +Q++ T+TLA GVNLPA VII+ + V GR + +L+
Sbjct: 388 MTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALD 447
Query: 302 MYKQMVGRAGRTGLQESGESIMLCKTMQDFLRFSSMMNAGPEPISSHMDPPTLVDLILEV 361
+ QM+GRAGR GE I++ + + + S++N PI S M L E+
Sbjct: 448 IL-QMLGRAGRPQYDTKGEGILIT-SHGELQYYLSLLNQQ-LPIESQMVSKLPDMLNAEI 504
Query: 362 VAANLCSSLEDVKTLIKHTLFYQ-LKSP 388
V N+ ++ + V L L+ + L+SP
Sbjct: 505 VLGNVQNAKDAVNWLGYAYLYIRMLRSP 532
Score = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 88/334 (26%), Positives = 158/334 (47%), Gaps = 43/334 (12%)
Query: 37 LNKKSIYICTIEKGSKLIGSLIQENRIDEIGLIVIDEFHMLNEPQRGPILECVVSKVLYL 96
L K +I I T EK L Q + I L V+DE H++ + GP+LE + S++ Y+
Sbjct: 1018 LGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGG-ENGPVLEVICSRMRYI 1076
Query: 97 ----KKSIQIFAMSATIGNINALSTFIE-GITYVENSRPTKHSEYVTVDKRVFQSFDGKS 151
++ I+I A+S+++ N ++ ++ T N P + + + F ++
Sbjct: 1077 SSQIERPIRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQT 1136
Query: 152 LTEIYADNLDYSLTGSGPDAVLHLVQGNLMVLIFCSSKIAC--------SNLALRLQFDR 203
A + +++T P V++F S+ + A +Q R
Sbjct: 1137 RLLSMAKPVYHAITKHSPKKP---------VIVFVPSRKQTRLTAIDILTTCAADIQRQR 1187
Query: 204 FPGTKEYKKQEKEDLIEALKEENDGKLSTNLEECILYGVAYHHADLTAGERRLIEEAYLA 263
F E +DLI L++ +D + L+E +L GV Y H L+ ERRL+E+ + +
Sbjct: 1188 FLHCTE------KDLIPYLEKLSD----STLKETLLNGVGYLHEGLSPMERRLVEQLFSS 1237
Query: 264 GTLQIICCTSTLAAGVNLPAQRVIIRDS--YVGR--DFISLNMYK--QMVGRAGRTGLQE 317
G +Q++ + +L G+N+ A VII D+ Y G+ ++ +Y QMVG A R +
Sbjct: 1238 GAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDD 1297
Query: 318 SGESIMLCK-TMQDFLRFSSMMNAGPEPISSHMD 350
G +++C+ + +DF F + P P+ SH+D
Sbjct: 1298 EGRCVIMCQGSKKDF--FKKFLYE-PLPVESHLD 1328
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 105 bits (263), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 104/388 (26%), Positives = 191/388 (49%), Gaps = 44/388 (11%)
Query: 24 AGVKGQYPPTKRQLNKKSIYICTIEKGSKLIGSLIQENRIDEIGLIVIDEFHMLNEPQRG 83
A + G + K +++ I +CT EK + + + LI++DE H+L++ RG
Sbjct: 166 AELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHD-DRG 224
Query: 84 PILECVVSKVL----YLKKSIQIFAMSATIGNINALSTFI-----EGITYVENS-RPTK- 132
P+LE +V++ + ++ +++ +SAT+ N ++TF+ +G+ Y +NS RP
Sbjct: 225 PVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPL 284
Query: 133 HSEYVTV-DKRVFQSFDGKSLTEIYADNLDYSLTGSGPDAVLHLVQGNLMVLIFCSSKIA 191
YV + +K+ + F + + EI + + + H + ++V + +
Sbjct: 285 EQTYVGITEKKAIKRF--QIMNEIVYEKI-----------MEHAGKNQVLVFVHSRKETG 331
Query: 192 CSNLALR---LQFDRFPGTKEYKKQEKEDLIEALKEENDGKLSTNLEECILYGVAYHHAD 248
+ A+R L+ D T +E E L+ E + + L++ + YG A HHA
Sbjct: 332 KTARAIRDMCLEKD----TLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAG 387
Query: 249 LTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYV-----GR--DFISLN 301
+T +R L+E+ + +Q++ T+TLA GVNLPA VII+ + V GR + +L+
Sbjct: 388 MTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALD 447
Query: 302 MYKQMVGRAGRTGLQESGESIMLCKTMQDFLRFSSMMNAGPEPISSHMDPPTLVDLILEV 361
+ QM+GRAGR GE I++ + + + S++N PI S M L E+
Sbjct: 448 IL-QMLGRAGRPQYDTKGEGILIT-SHGELQYYLSLLNQQ-LPIESQMVSKLPDMLNAEI 504
Query: 362 VAANLCSSLEDVKTLIKHTLFYQ-LKSP 388
V N+ ++ + V L L+ + L+SP
Sbjct: 505 VLGNVQNAKDAVNWLGYAYLYIRMLRSP 532
Score = 98.2 bits (243), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 88/334 (26%), Positives = 158/334 (47%), Gaps = 43/334 (12%)
Query: 37 LNKKSIYICTIEKGSKLIGSLIQENRIDEIGLIVIDEFHMLNEPQRGPILECVVSKVLYL 96
L K +I I T EK L Q + I L V+DE H++ + GP+LE + S++ Y+
Sbjct: 1018 LGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGG-ENGPVLEVICSRMRYI 1076
Query: 97 ----KKSIQIFAMSATIGNINALSTFIE-GITYVENSRPTKHSEYVTVDKRVFQSFDGKS 151
++ I+I A+S+++ N ++ ++ T N P + + + F ++
Sbjct: 1077 SSQIERPIRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQT 1136
Query: 152 LTEIYADNLDYSLTGSGPDAVLHLVQGNLMVLIFCSSKIAC--------SNLALRLQFDR 203
A + +++T P V++F S+ + A +Q R
Sbjct: 1137 RLLSMAKPVYHAITKHSPKKP---------VIVFVPSRKQTRLTAIDILTTCAADIQRQR 1187
Query: 204 FPGTKEYKKQEKEDLIEALKEENDGKLSTNLEECILYGVAYHHADLTAGERRLIEEAYLA 263
F E +DLI L++ +D + L+E +L GV Y H L+ ERRL+E+ + +
Sbjct: 1188 FLHCTE------KDLIPYLEKLSD----STLKETLLNGVGYLHEGLSPMERRLVEQLFSS 1237
Query: 264 GTLQIICCTSTLAAGVNLPAQRVIIRDS--YVGR--DFISLNMYK--QMVGRAGRTGLQE 317
G +Q++ + +L G+N+ A VII D+ Y G+ ++ +Y QMVG A R +
Sbjct: 1238 GAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDD 1297
Query: 318 SGESIMLCK-TMQDFLRFSSMMNAGPEPISSHMD 350
G +++C+ + +DF F + P P+ SH+D
Sbjct: 1298 EGRCVIMCQGSKKDF--FKKFLYE-PLPVESHLD 1328
>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 = 67.8 bits (164), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 79/312 (25%), Positives = 132/312 (42%), Gaps = 60/312 (19%)
Query: 65 EIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINALSTFIEGI-- 122
E+ ++ DE H + + +RG + E ++ L ++ +SATI N + +I I
Sbjct: 192 EVAWVIFDEVHYMRDKERGVVWE---ETIILLPDKVRYVFLSATIPNAMEFAEWICKIHS 248
Query: 123 ----TYVENSRPTK--------HSE--YVTVD-KRVFQSFDGK----SLTEIYADNLDY- 162
N RPT H + Y+ VD K F+ + + S++ D+ +
Sbjct: 249 QPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNST 308
Query: 163 -------------SLTGSGPDAVLHLVQGNLM-----VLIFCSSKIACSNLALRLQFDRF 204
S G + +V+ V++F SK C LAL++ F
Sbjct: 309 DSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDF 368
Query: 205 PGTKEYKKQEKEDLIE------ALKEENDGKLS--TNLEECILYGVAYHHADLTAGERRL 256
EKE L + AL E D +L ++ + G+ HH+ L + +
Sbjct: 369 -----NSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEV 423
Query: 257 IEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRD--SYVGRDF--ISLNMYKQMVGRAGR 312
IE + G L+++ T T + G+N+PA+ V+ + G+ F +S Y QM GRAGR
Sbjct: 424 IEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGR 483
Query: 313 TGLQESGESIML 324
GL + G IM+
Sbjct: 484 RGLDDRGIVIMM 495
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 67.4 bits (163), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 79/312 (25%), Positives = 132/312 (42%), Gaps = 60/312 (19%)
Query: 65 EIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINALSTFIEGI-- 122
E+ ++ DE H + + +RG + E ++ L ++ +SATI N + +I I
Sbjct: 290 EVAWVIFDEVHYMRDKERGVVWE---ETIILLPDKVRYVFLSATIPNAMEFAEWICKIHS 346
Query: 123 ----TYVENSRPTK--------HSE--YVTVD-KRVFQSFDGK----SLTEIYADNLDY- 162
N RPT H + Y+ VD K F+ + + S++ D+ +
Sbjct: 347 QPCHIVYTNFRPTPLQHYLFPAHGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNST 406
Query: 163 -------------SLTGSGPDAVLHLVQGNLM-----VLIFCSSKIACSNLALRLQFDRF 204
S G + +V+ V++F SK C LAL++ F
Sbjct: 407 DSRGKKGQTYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDF 466
Query: 205 PGTKEYKKQEKEDLIE------ALKEENDGKLS--TNLEECILYGVAYHHADLTAGERRL 256
EKE L + AL E D +L ++ + G+ HH+ L + +
Sbjct: 467 -----NSDDEKEALTKIFNNAIALLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEV 521
Query: 257 IEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRD--SYVGRDF--ISLNMYKQMVGRAGR 312
IE + G L+++ T T + G+N+PA+ V+ + G+ F +S Y QM GRAGR
Sbjct: 522 IEILFQEGFLKVLFATETFSIGLNMPAKTVVFTSVRKWDGQQFRWVSGGEYIQMSGRAGR 581
Query: 313 TGLQESGESIML 324
GL + G IM+
Sbjct: 582 RGLDDRGIVIMM 593
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 52/194 (26%), Positives = 85/194 (43%), Gaps = 21/194 (10%)
Query: 140 DKRVFQSFDGKSLTEIYADNLDYSLTGSGPDAVLHLVQGNLM-VLIFCSSKIACSNLALR 198
+KR F + DG S + P+ V +L + L+ +++F SK C A
Sbjct: 309 NKRKFFTQDGPS-------------KKTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADW 355
Query: 199 LQFDRFPGTKEYKKQE---KEDLIEALKEENDGKLSTNLEECILYGVAYHHADLTAGERR 255
L+ F KE + ++ + KE+ D + G+A HH L +
Sbjct: 356 LEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKE 415
Query: 256 LIEEAYLAGTLQIICCTSTLAAGVNLPAQRVII----RDSYVGRDFISLNMYKQMVGRAG 311
LIE + G ++++ T T A G+NLP + VI + G ++ + QM GRAG
Sbjct: 416 LIEILFSKGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAG 475
Query: 312 RTGLQESGESIMLC 325
R GL +G I++
Sbjct: 476 RRGLDSTGTVIVMA 489
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 63 IDEIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIGNINALSTFI 119
I ++ ++ DE H +N+ RG + E V ++ L + ++ +SAT+ N + +I
Sbjct: 145 IRDVEFVIFDEVHYVNDQDRGVVWEEV---IIMLPQHVKFILLSATVPNTYEFANWI 198
>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2V1X|B Chain B, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2WWY|A Chain A, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
pdb|2WWY|B Chain B, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
Length = 591
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 59/129 (45%), Gaps = 10/129 (7%)
Query: 210 YKKQEKEDLIEALKEENDGKLSTNLEECILYGVAYHHADLTAGERRLIEEAYLAGTLQII 269
YK Q +I +++ +++ +L+ ++ AYH A+L ++ + + A +Q++
Sbjct: 265 YKGQS--GIIYCFSQKDSEQVTVSLQNLGIHAGAYH-ANLEPEDKTTVHRKWSANEIQVV 321
Query: 270 CCTSTLAAGVNLPAQRVIIRDSYVGRDFISLNMYKQMVGRAGRTGLQESGESIMLCKTMQ 329
T G++ P R +I S S+ Y Q GRAGR ++ +L
Sbjct: 322 VATVAFGMGIDKPDVRFVIHHSMSK----SMENYYQESGRAGRDDMK---ADCILYYGFG 374
Query: 330 DFLRFSSMM 338
D R SSM+
Sbjct: 375 DIFRISSMV 383
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 242 VAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDFISLN 301
A +HA L R ++E + LQI+ T G+N P R ++ + R+ S
Sbjct: 263 AAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFD-IPRNIES-- 319
Query: 302 MYKQMVGRAGRTGL 315
Y Q GRAGR GL
Sbjct: 320 -YYQETGRAGRDGL 332
>pdb|2DFL|A Chain A, Crystal Structure Of Left-Handed Rada Filament
pdb|2Z43|A Chain A, Structure Of A Twinned Crystal Of Rada
pdb|2Z43|B Chain B, Structure Of A Twinned Crystal Of Rada
pdb|2Z43|C Chain C, Structure Of A Twinned Crystal Of Rada
pdb|2ZUB|A Chain A, Left Handed Rada
pdb|2ZUB|B Chain B, Left Handed Rada
pdb|2ZUC|A Chain A, Crystal Structure Of Left-Handed Rada Filament
pdb|2ZUC|B Chain B, Crystal Structure Of Left-Handed Rada Filament
pdb|2ZUD|A Chain A, Crystal Structure Of Left-Handed Rada Filament
pdb|2ZUD|B Chain B, Crystal Structure Of Left-Handed Rada Filament
Length = 324
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 604 NLRALMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAK 661
N++ + DLPG+ +L+ AGYSSLE +A A +++ +PL +A+ +I A+
Sbjct: 10 NIKTINDLPGISQTVINKLIEAGYSSLETLAVASPQDLSVAA-GIPLSTAQKIIKEAR 66
>pdb|2BKE|A Chain A, Conformational Flexibility Revealed By The Crystal
Structure Of A Crenarchaeal Rada
Length = 324
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 1/58 (1%)
Query: 604 NLRALMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAK 661
N++ + DLPG+ +L+ AGYSSLE +A A +++ +PL +A+ +I A+
Sbjct: 10 NIKTINDLPGISQTVINKLIEAGYSSLETLAVASPQDLSVAA-GIPLSTAQKIIKEAR 66
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 242 VAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDFISLN 301
A +HA L R ++E + LQI+ T G+N P R ++ + R+ S
Sbjct: 263 AAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGMGINKPNVRFVVHFD-IPRNIES-- 319
Query: 302 MYKQMVGRAGRTGL 315
Y Q GRAGR GL
Sbjct: 320 -YYQETGRAGRDGL 332
>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 = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 605 LRALMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAK 661
+R++ DLPGV A +L AGY +LE IA A E+ ++ + +A +I AA+
Sbjct: 34 IRSIEDLPGVGPATAEKLREAGYDTLEAIAVASPIEL-KEVAGISEGTALKIIQAAR 89
>pdb|2WAX|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAX|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|A Chain A, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
pdb|2WAY|C Chain C, Structure Of The Human Ddx6 C-Terminal Domain In Complex
With An Edc3-Fdf Peptide
Length = 193
Score = 33.5 bits (75), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 31/115 (26%), Positives = 48/115 (41%), Gaps = 12/115 (10%)
Query: 240 YGVAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDFIS 299
Y Y HA + R + + G + + CT G+++ A V+I DF
Sbjct: 69 YSCFYIHAKMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVI-----NFDFPK 123
Query: 300 L-NMYKQMVGRAGRTGLQESGESIMLCKTMQDFLRFSSM---MNAGPEPISSHMD 350
L Y +GR+GR G G +I L T D S+ + +PI S++D
Sbjct: 124 LAETYLHRIGRSGRFG--HLGLAINLI-TYDDRFNLKSIEEQLGTEIKPIPSNID 175
>pdb|3IRV|A Chain A, Crystal Structure Of Cysteine Hydrolase Pspph_2384 From
Pseudomonas Syringae Pv. Phaseolicola 1448a
Length = 233
Score = 32.7 bits (73), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 23/99 (23%), Positives = 46/99 (46%), Gaps = 8/99 (8%)
Query: 202 DRFPGTKEYKKQEKEDL--IEALKEENDGKLSTNLEECILYGVAYHHADL-TAGERRLIE 258
D +P + + D+ IEAL ++D + L + +H+ DL T R ++
Sbjct: 86 DLYPNVDQILARHDPDVEVIEALAPQSDDVIVDKL-----FYSGFHNTDLDTVLRARDVD 140
Query: 259 EAYLAGTLQIICCTSTLAAGVNLPAQRVIIRDSYVGRDF 297
+ GT+ +CC +T+ GV+ + + + D+ D+
Sbjct: 141 TIIVCGTVTNVCCETTIRDGVHREYKVIALSDANAAMDY 179
>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 = 32.3 bits (72), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 22/37 (59%)
Query: 246 HADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLP 282
H D++ GER + A+ G ++++ T A G+++P
Sbjct: 59 HGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIP 95
>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 = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 12/43 (27%), Positives = 25/43 (58%)
Query: 246 HADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPAQRVII 288
H DL+ GER + A+ G ++++ T A G+++P +++
Sbjct: 62 HGDLSQGERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVV 104
>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 = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 4/93 (4%)
Query: 225 ENDGKLSTNLEECILYG-VAYHHADLTAGERRLIEEAYLAGTLQIICCTSTLAAGVNLPA 283
EN K + L E + +A H + E + + ++ CT+ + G+++P
Sbjct: 823 ENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPT 882
Query: 284 QRVIIRDSYVGRDFISLNMYKQMVGRAGRTGLQ 316
II + D L Q+ GR GR+ Q
Sbjct: 883 ANTIIIERA---DHFGLAQLHQLRGRVGRSHHQ 912
>pdb|3NTU|A Chain A, Rada Recombinase D302k Mutant In Complex With Amp-Pnp
Length = 319
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 607 ALMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAK 661
L DLPGV A +L+ AGY IA A E+ I + ++A +I A+
Sbjct: 1 GLTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELT-DIEGISEKAAAKMIMGAR 54
>pdb|1T4G|A Chain A, Atpase In Complex With Amp-pnp
pdb|1XU4|A Chain A, Atpase In Complex With Amp-Pnp, Magnesium And Potassium
Co-F
pdb|2FPK|A Chain A, Rada Recombinase In Complex With Adp
pdb|2FPL|A Chain A, Rada Recombinase In Complex With Amp-Pnp And Low
Concentration Of K+
pdb|2FPM|A Chain A, Rada Recombinase In Complex With Amp-Pnp And High
Concentration Of K+
pdb|2B21|A Chain A, Rada Recombinase In Complex With Amppnp At Ph 6.0
pdb|2I1Q|A Chain A, Rada Recombinase In Complex With Calcium
pdb|3FYH|A Chain A, Recombinase In Complex With Adp And Metatungstate
Length = 322
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 608 LMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAK 661
L DLPGV A +L+ AGY IA A E+ I + ++A +I A+
Sbjct: 5 LTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELT-DIEGISEKAAAKMIMGAR 57
>pdb|2F1H|A Chain A, Recombinase In Complex With Amp-pnp And Potassium
pdb|2F1I|A Chain A, Recombinase In Complex With Amp-pnp
pdb|2F1J|A Chain A, Recombinase In Complex With Adp
Length = 322
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 608 LMDLPGVKIGRARQLLNAGYSSLELIARADAKEMVAKIRHLPLRSARNLISAAK 661
L DLPGV A +L+ AGY IA A E+ I + ++A +I A+
Sbjct: 5 LTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELT-DIEGISEKAAAKMIMGAR 57
>pdb|4DXY|A Chain A, Crystal Structures Of Cyp101d2 Y96a Mutant
Length = 417
Score = 30.0 bits (66), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 34/131 (25%), Positives = 54/131 (41%), Gaps = 11/131 (8%)
Query: 2 VHEKYQSLAKAAEEFKFYLEEYAGVKGQYPPTKRQLNKKSIYICTIEKGSKLIGSLIQEN 61
V E Y + + E F +E AG K Q PTK + + Y ++KG L E+
Sbjct: 72 VKEVYSDPTRFSSEVIFLPKE-AGEKAQMVPTKMDPPEHTPYRKALDKGLNLAKIRKVED 130
Query: 62 RIDEIGLIVIDEFHMLNEPQRGPILECVVSKVLYLKKSIQIFAMSATIG--NINALSTFI 119
++ E+ +ID F RG EC + + +F A + +I LS +
Sbjct: 131 KVREVASSLIDSFA-----ARG---ECDFAAEYAELFPVHVFMALADLPLEDIPVLSEYA 182
Query: 120 EGITYVENSRP 130
+T E + P
Sbjct: 183 RQMTRPEGNTP 193
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
0.321 0.136 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,814,351
Number of Sequences: 62578
Number of extensions: 744944
Number of successful extensions: 1798
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1742
Number of HSP's gapped (non-prelim): 42
length of query: 693
length of database: 14,973,337
effective HSP length: 106
effective length of query: 587
effective length of database: 8,340,069
effective search space: 4895620503
effective search space used: 4895620503
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)