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= psy2764
(419 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 385 bits (988), Expect = e-107, Method: Compositional matrix adjust.
Identities = 199/420 (47%), Positives = 268/420 (63%), Gaps = 44/420 (10%)
Query: 43 QTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKT 102
+ EWA ++D++ + +FD +P A +WPFELD FQK+A+ LE+ + VFV AHTSAGKT
Sbjct: 9 KKEWAHVVDLNHKIENFDELIPNPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKT 68
Query: 103 VIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDV--GLVTGDFQINTTASCLV 160
V+AEYAIA++ + T+TIYTSPIKALSNQK+RDF+ETF DV GL+TGD QIN A+CL+
Sbjct: 69 VVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDVQINPDANCLI 128
Query: 161 MTTEILRSMLYRGSDVLRDLEYVIFDEVHYINDSERGHVWEEVLILLPKEVCIVMLSATV 220
MTTEILRSMLYRG+D++RD+E+VIFDEVHY+ND +RG VWEEV+I+LP+ V ++LSATV
Sbjct: 129 MTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLSATV 188
Query: 221 PNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLYVG----PVLEKNQLFL--------- 267
PNT EFA+W+G TK+ +YV+ST KRPVPL+ ++ PV+ +N FL
Sbjct: 189 PNTYEFANWIGRTKQKNIYVISTPKRPVPLEINIWAKKELIPVINQNSEFLEANFRKHKE 248
Query: 268 ----------------------IREAEGEFLTRGYLAAKEVKCRKQLEKXXXXXXKLNGP 305
R G TR + R + G
Sbjct: 249 ILNGESAKGAPSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGS 308
Query: 306 FTR------GAEKNLFISFLNYLRKSQNLPVVLFTLSRKRCDQNAANLLSMDFSTATEKS 359
R G K + +NYLRK + LP+V+F S+KRC++ A L ++F EKS
Sbjct: 309 NKRKFFTQDGPSKKTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKS 368
Query: 360 KIHRFFQDSIRNLQNEDDRALPQVKRLEQLLKNGIGVHHSGILPILKEIVEMLFQKGLVK 419
+IH F + SI L+ E DR LPQ+ + LL+ GI VHH G+LPI+KE++E+LF KG +K
Sbjct: 369 QIHMFIEKSITRLKKE-DRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIK 427
>pdb|3L9O|A Chain A, Crystal Structure Of Mtr4, A Co-Factor Of The Nuclear
Exosome
Length = 1108
Score = 318 bits (815), Expect = 4e-87, Method: Compositional matrix adjust.
Identities = 163/359 (45%), Positives = 226/359 (62%), Gaps = 10/359 (2%)
Query: 67 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 126
A T+PF LD FQ AI ++ V V+AHTSAGKTV+AEYAIA S +K R IYTSPIK
Sbjct: 178 ARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIK 237
Query: 127 ALSNQKYRDFRETFQDVGLVTGDFQINTTASCLVMTTEILRSMLYRGSDVLRDLEYVIFD 186
ALSNQKYR+ F DVGL+TGD IN A CLVMTTEILRSMLYRGS+V+R++ +VIFD
Sbjct: 238 ALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFD 297
Query: 187 EVHYINDSERGHVWEEVLILLPKEVCIVMLSATVPNTLEFADWVGNTKKTKVYVVSTLKR 246
EVHY+ D ERG VWEE +ILLP +V V LSAT+PN +EFA+W+ ++V T R
Sbjct: 298 EVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFR 357
Query: 247 PVPLKHFLYVGPVLEKNQLFLIREAEGEFLTRGYLAAKEVKCRK------QLEKXXXXXX 300
P PL+H+L+ + ++L+ + + F + A + +
Sbjct: 358 PTPLQHYLFPA---HGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQ 414
Query: 301 KLNGPFTRGAEKNLFISFLNYLRKSQNLPVVLFTLSRKRCDQNAANLLSMDFSTATEKSK 360
G +G K + + K + PV++F+ S++ C++ A + +DF++ EK
Sbjct: 415 TYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEA 474
Query: 361 IHRFFQDSIRNLQNEDDRALPQVKRLEQLLKNGIGVHHSGILPILKEIVEMLFQKGLVK 419
+ + F ++I L E DR LPQ+K + LL+ GIG+HHSG+LPILKE++E+LFQ+G +K
Sbjct: 475 LTKIFNNAIA-LLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLK 532
>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 = 318 bits (814), Expect = 4e-87, Method: Compositional matrix adjust.
Identities = 163/359 (45%), Positives = 226/359 (62%), Gaps = 10/359 (2%)
Query: 67 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 126
A T+PF LD FQ AI ++ V V+AHTSAGKTV+AEYAIA S +K R IYTSPIK
Sbjct: 80 ARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIK 139
Query: 127 ALSNQKYRDFRETFQDVGLVTGDFQINTTASCLVMTTEILRSMLYRGSDVLRDLEYVIFD 186
ALSNQKYR+ F DVGL+TGD IN A CLVMTTEILRSMLYRGS+V+R++ +VIFD
Sbjct: 140 ALSNQKYRELLAEFGDVGLMTGDITINPDAGCLVMTTEILRSMLYRGSEVMREVAWVIFD 199
Query: 187 EVHYINDSERGHVWEEVLILLPKEVCIVMLSATVPNTLEFADWVGNTKKTKVYVVSTLKR 246
EVHY+ D ERG VWEE +ILLP +V V LSAT+PN +EFA+W+ ++V T R
Sbjct: 200 EVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFR 259
Query: 247 PVPLKHFLYVGPVLEKNQLFLIREAEGEFLTRGYLAAKEVKCRK------QLEKXXXXXX 300
P PL+H+L+ + ++L+ + + F + A + +
Sbjct: 260 PTPLQHYLFPA---HGDGIYLVVDEKSTFREENFQKAMASISNQIGDDPNSTDSRGKKGQ 316
Query: 301 KLNGPFTRGAEKNLFISFLNYLRKSQNLPVVLFTLSRKRCDQNAANLLSMDFSTATEKSK 360
G +G K + + K + PV++F+ S++ C++ A + +DF++ EK
Sbjct: 317 TYKGGSAKGDAKGDIYKIVKMIWKKKYNPVIVFSFSKRDCEELALKMSKLDFNSDDEKEA 376
Query: 361 IHRFFQDSIRNLQNEDDRALPQVKRLEQLLKNGIGVHHSGILPILKEIVEMLFQKGLVK 419
+ + F ++I L E DR LPQ+K + LL+ GIG+HHSG+LPILKE++E+LFQ+G +K
Sbjct: 377 LTKIFNNAIA-LLPETDRELPQIKHILPLLRRGIGIHHSGLLPILKEVIEILFQEGFLK 434
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 98.2 bits (243), Expect = 8e-21, Method: Compositional matrix adjust.
Identities = 91/353 (25%), Positives = 165/353 (46%), Gaps = 58/353 (16%)
Query: 78 QKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAI-ALSQNHKTRTIYTSPIKALSNQKYRD 135
Q +A+ K L E N + +T+ T +GKT+IAE I + + + IY +P++AL+N+KY
Sbjct: 35 QTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAIYVTPLRALTNEKYLT 94
Query: 136 FRE----TFQDVGLVTGDFQINTT----ASCLVMTTEILRSMLYRGSDVLRDLEYVIFDE 187
F++ F+ V + +GD+ + ++ T E L S+ + L ++ Y + DE
Sbjct: 95 FKDWELIGFK-VAMTSGDYDTDDAWLKNYDIIITTYEKLDSLWRHRPEWLNEVNYFVLDE 153
Query: 188 VHYINDSERGHVWEEVLILLPKEVCIVMLSATVPNTLEFADWVGNTKKTKVYVVSTLKRP 247
+HY+ND ERG V E V I K ++ LSAT+ N + A W+G V+T RP
Sbjct: 154 LHYLNDPERGPVVESVTI-RAKRRNLLALSATISNYKQIAKWLGAEP------VATNWRP 206
Query: 248 VPLKHFLYVGPVLEKNQLFLIREAEGEFLTRGYLAAKEVKCRKQLEKXXXXXXKLNGPFT 307
VP L G + + K + K++G
Sbjct: 207 VP--------------------------LIEGVIYPERKKKEYNVIFKDNTTKKVHG--- 237
Query: 308 RGAEKNLFISFLNYLRKSQNLPVVLFTLSRKRCDQNAANLLS-MDFSTATEKSKIHRFFQ 366
+ + L+ L S+N V++F SRK + A + + M+F + E +
Sbjct: 238 ---DDAIIAYTLDSL--SKNGQVLVFRNSRKMAESTALKIANYMNFVSLDENA-----LS 287
Query: 367 DSIRNLQNEDDRALPQVKRLEQLLKNGIGVHHSGILPILKEIVEMLFQKGLVK 419
+ ++ L + ++ + + L+ L+ G+ HH+G+ L++++E F++ +K
Sbjct: 288 EILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEGFRQRKIK 340
>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
Length = 1724
Score = 88.6 bits (218), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 92/351 (26%), Positives = 156/351 (44%), Gaps = 72/351 (20%)
Query: 89 NHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD---- 142
++VFV A T +GKT+ AE+AI L Q+ + R +Y +P++AL+ Q Y D+ E FQD
Sbjct: 943 DNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNK 1002
Query: 143 -VGLVTG----DFQINTTASCLVMTTEI--LRSMLYRGSDVLRDLEYVIFDEVHYINDSE 195
V L+TG D ++ + ++ T E + S ++ ++++ + DEVH I E
Sbjct: 1003 KVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIG-GE 1061
Query: 196 RGHVWEEVLILL-------PKEVCIVMLSATVPNTLEFADWVGNTKKTKVYVVSTLKRPV 248
G V E + + + + IV LS+++ N + A W+G T + RPV
Sbjct: 1062 NGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLG-CSATSTFNFHPNVRPV 1120
Query: 249 PLKHFLYVGPVLEKNQLFLIREAEGEFLTRGYLAAKEVKCRKQLEKXXXXXXKLNGPFTR 308
PL+ L++ Q F I + L+ AK V
Sbjct: 1121 PLE--LHI-------QGFNISHTQTRLLS----MAKPV---------------------- 1145
Query: 309 GAEKNLFISFLNYLRKSQNLPVVLFTLSRKRCDQNAANLLSMDFSTATEKSKIHRFFQDS 368
+ + S PV++F SRK+ A ++L+ + + +H +D
Sbjct: 1146 ---------YHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDL 1196
Query: 369 IRNLQNEDDRALPQVKRLEQLLKNGIGVHHSGILPILKEIVEMLFQKGLVK 419
I L+ D L++ L NG+G H G+ P+ + +VE LF G ++
Sbjct: 1197 IPYLEKLSDST------LKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQ 1241
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 84/362 (23%), Positives = 148/362 (40%), Gaps = 86/362 (23%)
Query: 85 LEEHNHVFVTAHTSAGKTVIA------EYAIALSQNHKT-----RTIYTSPIKALSNQKY 133
LE ++ + A T AGKT +A E ++ + + IY +P+++L +
Sbjct: 92 LETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMV 151
Query: 134 RDFRETFQDVGL----VTGDFQIN----TTASCLVMTTEILRSMLYRGSD--VLRDLEYV 183
F + G+ +TGD Q+ + +V T E + +G + + + +
Sbjct: 152 GSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLI 211
Query: 184 IFDEVHYINDSERGHVWEEVLI-------LLPKEVCIVMLSATVPNTLEFADWVGNTKKT 236
I DE+H ++D +RG V E ++ + ++V ++ LSAT+PN + A ++
Sbjct: 212 ILDEIHLLHD-DRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAK 270
Query: 237 KVYVVSTLKRPVPLKHFLYVGPVLEKNQLFLIREAEGEFLTRGYLAAKEVKCRKQLEKXX 296
++ RPVPL+ YVG + EK + + + E+ K +E
Sbjct: 271 GLFYFDNSFRPVPLEQ-TYVG-ITEKKAI------------KRFQIMNEIVYEKIMEH-- 314
Query: 297 XXXXKLNGPFTRGAEKNLFISFLNYLRKSQNLPVVLFTLSRKRCDQNAANLLSMDFSTAT 356
A KN V++F SRK + A + M
Sbjct: 315 -------------AGKN---------------QVLVFVHSRKETGKTARAIRDM----CL 342
Query: 357 EKSKIHRFFQD---SIRNLQNEDDRALPQVKRLE--QLLKNGIGVHHSGILPILKEIVEM 411
EK + F ++ S L+ E + Q K LE LL G +HH+G+ + + +VE
Sbjct: 343 EKDTLGLFLREGSASTEVLRTEAE----QCKNLELKDLLPYGFAIHHAGMTRVDRTLVED 398
Query: 412 LF 413
LF
Sbjct: 399 LF 400
>pdb|4F91|B Chain B, Brr2 Helicase Region
Length = 1724
Score = 88.6 bits (218), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 92/351 (26%), Positives = 156/351 (44%), Gaps = 72/351 (20%)
Query: 89 NHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRTIYTSPIKALSNQKYRDFRETFQD---- 142
++VFV A T +GKT+ AE+AI L Q+ + R +Y +P++AL+ Q Y D+ E FQD
Sbjct: 943 DNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNK 1002
Query: 143 -VGLVTG----DFQINTTASCLVMTTEI--LRSMLYRGSDVLRDLEYVIFDEVHYINDSE 195
V L+TG D ++ + ++ T E + S ++ ++++ + DEVH I E
Sbjct: 1003 KVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIG-GE 1061
Query: 196 RGHVWEEVLILL-------PKEVCIVMLSATVPNTLEFADWVGNTKKTKVYVVSTLKRPV 248
G V E + + + + IV LS+++ N + A W+G T + RPV
Sbjct: 1062 NGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLG-CSATSTFNFHPNVRPV 1120
Query: 249 PLKHFLYVGPVLEKNQLFLIREAEGEFLTRGYLAAKEVKCRKQLEKXXXXXXKLNGPFTR 308
PL+ L++ Q F I + L+ AK V
Sbjct: 1121 PLE--LHI-------QGFNISHTQTRLLS----MAKPV---------------------- 1145
Query: 309 GAEKNLFISFLNYLRKSQNLPVVLFTLSRKRCDQNAANLLSMDFSTATEKSKIHRFFQDS 368
+ + S PV++F SRK+ A ++L+ + + +H +D
Sbjct: 1146 ---------YHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDL 1196
Query: 369 IRNLQNEDDRALPQVKRLEQLLKNGIGVHHSGILPILKEIVEMLFQKGLVK 419
I L+ D L++ L NG+G H G+ P+ + +VE LF G ++
Sbjct: 1197 IPYLEKLSDST------LKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQ 1241
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 84/362 (23%), Positives = 148/362 (40%), Gaps = 86/362 (23%)
Query: 85 LEEHNHVFVTAHTSAGKTVIA------EYAIALSQNHKT-----RTIYTSPIKALSNQKY 133
LE ++ + A T AGKT +A E ++ + + IY +P+++L +
Sbjct: 92 LETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMV 151
Query: 134 RDFRETFQDVGL----VTGDFQIN----TTASCLVMTTEILRSMLYRGSD--VLRDLEYV 183
F + G+ +TGD Q+ + +V T E + +G + + + +
Sbjct: 152 GSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLI 211
Query: 184 IFDEVHYINDSERGHVWEEVLI-------LLPKEVCIVMLSATVPNTLEFADWVGNTKKT 236
I DE+H ++D +RG V E ++ + ++V ++ LSAT+PN + A ++
Sbjct: 212 ILDEIHLLHD-DRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAK 270
Query: 237 KVYVVSTLKRPVPLKHFLYVGPVLEKNQLFLIREAEGEFLTRGYLAAKEVKCRKQLEKXX 296
++ RPVPL+ YVG + EK + + + E+ K +E
Sbjct: 271 GLFYFDNSFRPVPLEQ-TYVG-ITEKKAI------------KRFQIMNEIVYEKIMEH-- 314
Query: 297 XXXXKLNGPFTRGAEKNLFISFLNYLRKSQNLPVVLFTLSRKRCDQNAANLLSMDFSTAT 356
A KN V++F SRK + A + M
Sbjct: 315 -------------AGKN---------------QVLVFVHSRKETGKTARAIRDM----CL 342
Query: 357 EKSKIHRFFQD---SIRNLQNEDDRALPQVKRLE--QLLKNGIGVHHSGILPILKEIVEM 411
EK + F ++ S L+ E + Q K LE LL G +HH+G+ + + +VE
Sbjct: 343 EKDTLGLFLREGSASTEVLRTEAE----QCKNLELKDLLPYGFAIHHAGMTRVDRTLVED 398
Query: 412 LF 413
LF
Sbjct: 399 LF 400
>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 = 87.4 bits (215), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 85/353 (24%), Positives = 164/353 (46%), Gaps = 69/353 (19%)
Query: 78 QKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFR 137
Q +A+ K+ ++ + T+AGKT++AE A+ +++Y P++AL+ +KY F+
Sbjct: 30 QAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEKYESFK 89
Query: 138 ETFQ---DVGLVTGDFQINTT--ASC--LVMTTEILRSMLYRGSDVLRDLEYVIFDEVHY 190
+ + +G+ TGD++ C +V T+E S++ + ++ + ++ DE+H
Sbjct: 90 KWEKIGLRIGISTGDYESRDEHLGDCDIIVTTSEKADSLIRNRASWIKAVSCLVVDEIHL 149
Query: 191 INDSERGHVWEEVLIL----LPKEVCIVMLSATVPNTLEFADWVGNTKKTKVYVVSTLKR 246
++ +RG E+L+ + K + ++ LSAT PN E A+W+ Y VS R
Sbjct: 150 LDSEKRGATL-EILVTKMRRMNKALRVIGLSATAPNVTEIAEWLDAD-----YYVSDW-R 202
Query: 247 PVPLKHFLYVGPVLEKNQLFLIREAEGEFLTRGYLAAKEVKCRKQLEKXXXXXXKLNGPF 306
PVPL + LE LF +G F T ++ VK + +E+
Sbjct: 203 PVPLVEGVLCEGTLE---LF-----DGAFST-----SRRVKFEELVEECV---------- 239
Query: 307 TRGAEKNLFISFLNYLRKSQNLPVVLFTLSRKRCDQNAANLLSMDFSTATEKSKIHRFFQ 366
++N V++F +R+ ++ A L S T K + +
Sbjct: 240 ------------------AENGGVLVFESTRRGAEKTAVKL-----SAITAKYVENEGLE 276
Query: 367 DSIRNLQNEDDRALPQVKRLEQLLKNGIGVHHSGILPILKEIVEMLFQKGLVK 419
+I +NE + + ++L + ++ G HH+G+L + +VE F++G +K
Sbjct: 277 KAILE-ENEGEMS----RKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNIK 324
>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 = 79.3 bits (194), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 52/180 (28%), Positives = 97/180 (53%), Gaps = 20/180 (11%)
Query: 87 EHNHVFVTAHTSAGKTVIAEYAIA---LSQNHKTRTIYTSPIKALSNQKYRDFRETFQDV 143
E + ++ T++GKT+IAE A+ L+Q K +Y P+KAL+ +K+++F++ ++ +
Sbjct: 38 EGKNALISIPTASGKTLIAEIAMVHRILTQGGKA--VYIVPLKALAEEKFQEFQD-WEKI 94
Query: 144 GL----VTGDFQINT----TASCLVMTTEILRSMLYRGSDVLRDLEYVIFDEVHYINDSE 195
GL TGD+ ++ T E S+L GS ++D++ ++ DE+H I +
Sbjct: 95 GLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRD 154
Query: 196 RGHVWEEVLILLPKEVCIVMLSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKHFLY 255
RG E +L + + I+ LSAT+ N E A+W+ ++ + RPV L+ ++
Sbjct: 155 RGATLEVILAHMLGKAQIIGLSATIGNPEELAEWLNAE------LIVSDWRPVKLRRGVF 208
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 25/39 (64%)
Query: 381 PQVKRLEQLLKNGIGVHHSGILPILKEIVEMLFQKGLVK 419
P ++L + ++ G+ HH+G+ + +VE F+KG++K
Sbjct: 284 PTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIK 322
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 46/175 (26%), Positives = 79/175 (45%), Gaps = 20/175 (11%)
Query: 69 TWPFELDVFQKQAIIKL------EEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYT 122
+ PF+L QK+A ++ E+ + + +GKTV+A+ AI + +T +
Sbjct: 364 SLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFM 423
Query: 123 SPIKALSNQKYRDFRETFQDVGLVTGDFQINTTASCLVMTTEILRSMLYRGS-DVLRDLE 181
P L+ Q YR E+F + TT S E ++S L G DV+
Sbjct: 424 VPTSILAIQHYRRTVESFSKFNIHVALLIGATTPS----EKEKIKSGLRNGQIDVVIGTH 479
Query: 182 YVIFDEVHY-------INDSER-GHVWEEVLILLPKEVCIVMLSAT-VPNTLEFA 227
+I ++VH+ I++ R G E L+ K V +++SAT +P ++ A
Sbjct: 480 ALIQEDVHFKNLGLVIIDEQHRFGVKQREALMNKGKMVDTLVMSATPIPRSMALA 534
>pdb|4HT4|A Chain A, Molecular Basis Of Vancomycin Resistance Transfer In
Staphylococcus Aureus
Length = 195
Score = 35.0 bits (79), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 38/172 (22%), Positives = 69/172 (40%), Gaps = 19/172 (11%)
Query: 134 RDFRET-FQDVGLVTGDFQINTTASCLVMTTEILRSMLYRGSDVLRDLEYVIFDEVHYIN 192
+DF+E F+D D+ +EIL + D +D EY ++++VH +
Sbjct: 31 KDFKENEFKDYSNKQCDY------------SEIL--LPNNADDKFKDREY-LWNKVHDVE 75
Query: 193 DSERGHVWEEVLILLPKEVCIVMLSATVPNTLEFADWVGNTKKTKVYVVSTLKRPVPLKH 252
+ + V E++I LP E ++ + EFA+ + N + + P H
Sbjct: 76 NRKNSQVAREIIIGLPNE---FDPNSNIELAKEFAESLSNEGXIVDLNIHKINEENPHAH 132
Query: 253 FLYVGPVLEKNQLFLIREAEGEFLTRGYLAAKEVKCRKQLEKXXXXXXKLNG 304
L L+KN F + +++ K + RK+ E + NG
Sbjct: 133 LLCTLRGLDKNNEFEPKRKGNDYIRDWNTKEKHNEWRKRWENVQNKHLEKNG 184
>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|B Chain B, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|C Chain C, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|D Chain D, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|E Chain E, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|F Chain F, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
Length = 494
Score = 34.7 bits (78), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 33/128 (25%), Positives = 55/128 (42%), Gaps = 18/128 (14%)
Query: 76 VFQKQAIIKLEEHNHVFVTAHTSAGKT----VIAEYAIALSQNHKTRTIYTSPIKALSNQ 131
++Q+ K +E N + V T GKT +IAEY + + + + +P K L Q
Sbjct: 12 IYQEVIYAKCKETNCLIVLP-TGLGKTLIAMMIAEYRLT---KYGGKVLMLAPTKPLVLQ 67
Query: 132 KYRDFRETF----QDVGLVTGDFQIN------TTASCLVMTTEILRSMLYRGSDVLRDLE 181
FR F + + +TG+ A +V T + + + L G L D+
Sbjct: 68 HAESFRRLFNLPPEKIVALTGEKSPEERSKAWARAKVIVATPQTIENDLLAGRISLEDVS 127
Query: 182 YVIFDEVH 189
++FDE H
Sbjct: 128 LIVFDEAH 135
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 39/161 (24%), Positives = 63/161 (39%), Gaps = 18/161 (11%)
Query: 77 FQKQAIIKLEEHNHVFVTAHTSAGKTVI-------AEYAIALSQNHKTRTIYTSPIKALS 129
QKQ I + V A T +GKT+ A Y + + + SP + L+
Sbjct: 51 IQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTDGLGVLIISPTRELA 110
Query: 130 NQKYRDFRETFQD----VGLVTG--DFQ-----INTTASCLVMTTEILRSMLYRGSDVLR 178
Q + R+ ++ GL+ G D + IN + +L+ M S
Sbjct: 111 YQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVSFHAT 170
Query: 179 DLEYVIFDEVHYINDSERGHVWEEVLILLPKEVCIVMLSAT 219
DL+ ++ DE I D V+ LPK+ ++ SAT
Sbjct: 171 DLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSAT 211
>pdb|2XLQ|A Chain A, Structural And Mechanistic Analysis Of The Magnesium-
Independent Aromatic Prenyltransferase Cloq From The
Clorobiocin Biosynthetic Pathway
pdb|2XLY|A Chain A, Structural And Mechanistic Analysis Of The Magnesium-
Independent Aromatic Prenyltransferase Cloq From The
Clorobiocin Biosynthetic Pathway
Length = 327
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 16/86 (18%)
Query: 180 LEYVIFDEVHYINDS--ERGHVWEEVLILLPKEVCIVMLSATVPNTLEFADWVGNTKKTK 237
L+ V F +H ++ S HV EEVL +P++ C+ + TL+ G+ ++
Sbjct: 184 LDTVQFARIHALSGSTPPAAHVVEEVLAYMPEDYCVAI-------TLDLHS--GDIERVC 234
Query: 238 VYVVSTLKRPVP-----LKHFLYVGP 258
Y + K +P + FL V P
Sbjct: 235 FYALKVPKNALPRIPTRIARFLEVAP 260
>pdb|2XM7|A Chain A, Structural And Mechanistic Analysis Of The Magnesium-
Independent Aromatic Prenyltransferase Cloq From The
Clorobiocin Biosynthetic Pathway
Length = 327
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 39/86 (45%), Gaps = 16/86 (18%)
Query: 180 LEYVIFDEVHYINDS--ERGHVWEEVLILLPKEVCIVMLSATVPNTLEFADWVGNTKKTK 237
L+ V F +H ++ S HV EEVL +P++ C+ + TL+ G+ ++
Sbjct: 184 LDTVQFARIHALSGSTPPAAHVVEEVLAYMPEDYCVAI-------TLDLHS--GDIERVC 234
Query: 238 VYVVSTLKRPVP-----LKHFLYVGP 258
Y + K +P + FL V P
Sbjct: 235 FYALKVPKNALPRIPTRIARFLEVAP 260
>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
pdb|1VEC|B Chain B, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
Length = 206
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 14/76 (18%), Positives = 40/76 (52%)
Query: 150 FQINTTASCLVMTTEILRSMLYRGSDVLRDLEYVIFDEVHYINDSERGHVWEEVLILLPK 209
+++ T ++ T + ++ +G + ++ ++ DE + + + E++++ LPK
Sbjct: 117 MRLDDTVHVVIATPGRILDLIKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPK 176
Query: 210 EVCIVMLSATVPNTLE 225
I++ SAT P +++
Sbjct: 177 NRQILLYSATFPLSVQ 192
>pdb|3N1U|A Chain A, Structure Of Putative Had Superfamily (Subfamily Iii A)
Hydrolase From Legionella Pneumophila
Length = 191
Score = 29.3 bits (64), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 191 INDSERGHVWEEV--LILLPKEVCIVMLSATVPNTLEFADW 229
+ND E ++ +++ L L+ + V +S VP LEFADW
Sbjct: 108 LNDDEFAYIGDDLPDLPLIQQVGLGVAVSNAVPQVLEFADW 148
>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 = 29.3 bits (64), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 52/235 (22%), Positives = 88/235 (37%), Gaps = 37/235 (15%)
Query: 25 EVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAK---------------VPIMAHT 69
E + P+ K+ Q ++ DV+ +LD A+ + +
Sbjct: 540 EENAPLHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFCDS 599
Query: 70 WPFELDVFQKQAIIKLEEHN------HVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTS 123
+PFE Q QAI + V GKT +A A L+ ++ +
Sbjct: 600 FPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLV 659
Query: 124 PIKALSNQKYRDFRETFQD----VGLVTGDFQINTTASCLVMTTE-----ILRSMLYRGS 174
P L+ Q Y +FR+ F + + +++ L E ++ + S
Sbjct: 660 PTTLLAQQHYDNFRDRFANWPVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQS 719
Query: 175 DV-LRDLEYVIFDEVHYINDSERGHVWEEVLILLPKEVCIVMLSAT-VPNTLEFA 227
DV +DL +I DE H G +E + + V I+ L+AT +P TL A
Sbjct: 720 DVKFKDLGLLIVDEEHRF-----GVRHKERIKAMRANVDILTLTATPIPRTLNMA 769
>pdb|4GX0|A Chain A, Crystal Structure Of The Gsuk L97d Mutant
pdb|4GX0|B Chain B, Crystal Structure Of The Gsuk L97d Mutant
pdb|4GX0|C Chain C, Crystal Structure Of The Gsuk L97d Mutant
pdb|4GX0|D Chain D, Crystal Structure Of The Gsuk L97d Mutant
pdb|4GX1|A Chain A, Crystal Structure Of The Gsuk Bound To Adp
pdb|4GX1|B Chain B, Crystal Structure Of The Gsuk Bound To Adp
pdb|4GX1|C Chain C, Crystal Structure Of The Gsuk Bound To Adp
pdb|4GX1|D Chain D, Crystal Structure Of The Gsuk Bound To Adp
pdb|4GX2|A Chain A, Gsuk Channel Bound To Nad
pdb|4GX2|B Chain B, Gsuk Channel Bound To Nad
pdb|4GX2|C Chain C, Gsuk Channel Bound To Nad
pdb|4GX2|D Chain D, Gsuk Channel Bound To Nad
Length = 565
Score = 28.1 bits (61), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 6/61 (9%)
Query: 67 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 126
H F +D + I KLE NH+FV + + A+ L + + +Y SP
Sbjct: 128 GHILIFGIDPITRTLIRKLESRNHLFVVVTDN------YDQALHLEEQEGFKVVYGSPTD 181
Query: 127 A 127
A
Sbjct: 182 A 182
>pdb|4GX5|A Chain A, Gsuk Channel
pdb|4GX5|B Chain B, Gsuk Channel
pdb|4GX5|C Chain C, Gsuk Channel
pdb|4GX5|D Chain D, Gsuk Channel
Length = 565
Score = 28.1 bits (61), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 6/61 (9%)
Query: 67 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 126
H F +D + I KLE NH+FV + + A+ L + + +Y SP
Sbjct: 128 GHILIFGIDPITRTLIRKLESRNHLFVVVTDN------YDQALHLEEQEGFKVVYGSPTD 181
Query: 127 A 127
A
Sbjct: 182 A 182
>pdb|4GVL|A Chain A, Crystal Structure Of The Gsuk Rck Domain
pdb|4GVL|B Chain B, Crystal Structure Of The Gsuk Rck Domain
pdb|4GVL|C Chain C, Crystal Structure Of The Gsuk Rck Domain
pdb|4GVL|D Chain D, Crystal Structure Of The Gsuk Rck Domain
Length = 462
Score = 28.1 bits (61), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 6/61 (9%)
Query: 67 AHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIK 126
H F +D + I KLE NH+FV + + A+ L + + +Y SP
Sbjct: 25 GHILIFGIDPITRTLIRKLESRNHLFVVVTDN------YDQALHLEEQEGFKVVYGSPTD 78
Query: 127 A 127
A
Sbjct: 79 A 79
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 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,682,930
Number of Sequences: 62578
Number of extensions: 457620
Number of successful extensions: 1088
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1053
Number of HSP's gapped (non-prelim): 33
length of query: 419
length of database: 14,973,337
effective HSP length: 101
effective length of query: 318
effective length of database: 8,652,959
effective search space: 2751640962
effective search space used: 2751640962
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: 53 (25.0 bits)