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= 000174
(1931 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3C4T|A Chain A, Structure Of Rnaseiiib And Dsrna Binding Domains Of Mouse
Dicer
Length = 265
Score = 152 bits (385), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 97/243 (39%), Positives = 138/243 (56%), Gaps = 15/243 (6%)
Query: 1592 FHALEDALKIKFKDRGLLVEAITHASRPSSGVS-CYQRLEFVGDAVLDHLITKHLFFSYT 1650
F E + +FK++ L++A THAS + ++ YQRLEF+GDA+LD+LITKHL+
Sbjct: 15 FETFEKKINYRFKNKAYLLQAFTHASYHYNTITDXYQRLEFLGDAILDYLITKHLYEDPR 74
Query: 1651 NLPPGRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLE------- 1703
PG LTDLR+A VNN FA +AVK+ H + + S L I DFVK LE
Sbjct: 75 QHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEMQGM 134
Query: 1704 --ELLKPGFNSFGLGDCKAPKVLGDIVESIAGAIFLDSGRDTSVVWQVFQPLLDPMVT-- 1759
EL + + D + PK +GDI ES+AGAI++DSG VVWQV+ P++ P++
Sbjct: 135 DSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLEVVWQVYYPMMQPLIEKF 194
Query: 1760 PETLPMHPVRELQERCQQQAEGLEYKASRSGNL-ATVEVYIDGVQVGVAQNPQKKMAQKL 1818
+P PVREL E + A+ + + G + TVEV G GV ++ ++A+
Sbjct: 195 SANVPRSPVRELLEMEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRS--YRIAKSA 252
Query: 1819 AAR 1821
AAR
Sbjct: 253 AAR 255
Score = 44.7 bits (104), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 46/92 (50%), Gaps = 4/92 (4%)
Query: 1374 LKDKINYPVP-ASKILEALTAASCQE---TFCYERAELLGDAYLKWVVSRFLFLKYPQKH 1429
+ KINY + +L+A T AS T Y+R E LGDA L +++++ L+ Q
Sbjct: 18 FEKKINYRFKNKAYLLQAFTHASYHYNTITDXYQRLEFLGDAILDYLITKHLYEDPRQHS 77
Query: 1430 EGQLTRMRQQMVSNLVLYQYALSKGLQSYIQA 1461
G LT +R +V+N + A+ Y +A
Sbjct: 78 PGVLTDLRSALVNNTIFASLAVKYDYHKYFKA 109
>pdb|2LRS|A Chain A, The Second Dsrbd Domain From A. Thaliana Dicer-like 1
Length = 71
Score = 147 bits (372), Expect = 4e-35, Method: Composition-based stats.
Identities = 62/70 (88%), Positives = 68/70 (97%)
Query: 1859 NDICLRRNWPMPLYRCVREGGPAHAKRFTYAVRVNTTDKGWTDECVGEPMPSVKKAKDSA 1918
NDICLR+NWPMP YRCV+EGGPAHAKRFT+ VRVNT+D+GWTDEC+GEPMPSVKKAKDSA
Sbjct: 1 NDICLRKNWPMPSYRCVKEGGPAHAKRFTFGVRVNTSDRGWTDECIGEPMPSVKKAKDSA 60
Query: 1919 AVLLLELLNK 1928
AVLLLELLNK
Sbjct: 61 AVLLLELLNK 70
>pdb|3C4B|A Chain A, Structure Of Rnaseiiib And Dsrna Binding Domains Of Mouse
Dicer
Length = 265
Score = 147 bits (371), Expect = 5e-35, Method: Compositional matrix adjust.
Identities = 97/243 (39%), Positives = 134/243 (55%), Gaps = 15/243 (6%)
Query: 1592 FHALEDALKIKFKDRGLLVEAITHASRPSSGVS-CYQRLEFVGDAVLDHLITKHLFFSYT 1650
F E + +FK++ L++A THAS + ++ YQRLEF+GDA+LD+LITKHL+
Sbjct: 15 FETFEKKINYRFKNKAYLLQAFTHASYHYNTITDXYQRLEFLGDAILDYLITKHLYEDPR 74
Query: 1651 NLPPGRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLE------- 1703
PG LTDLR+A VNN FA +AVK+ H + + S L I DFVK LE
Sbjct: 75 QHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVKFQLEKNEXQGX 134
Query: 1704 --ELLKPGFNSFGLGDCKAPKVLGDIVESIAGAIFLDSGRDTSVVWQVFQPLLDPMVT-- 1759
EL + + D + PK GDI ES+AGAI+ DSG VVWQV+ P P++
Sbjct: 135 DSELRRSEEDEEKEEDIEVPKAXGDIFESLAGAIYXDSGXSLEVVWQVYYPXXQPLIEKF 194
Query: 1760 PETLPMHPVRELQERCQQQAEGLEYKASRSGNL-ATVEVYIDGVQVGVAQNPQKKMAQKL 1818
+P PVREL E + A+ + + G + TVEV G GV ++ ++A+
Sbjct: 195 SANVPRSPVRELLEXEPETAKFSPAERTYDGKVRVTVEVVGKGKFKGVGRS--YRIAKSA 252
Query: 1819 AAR 1821
AAR
Sbjct: 253 AAR 255
Score = 45.1 bits (105), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 46/92 (50%), Gaps = 4/92 (4%)
Query: 1374 LKDKINYPVP-ASKILEALTAASCQE---TFCYERAELLGDAYLKWVVSRFLFLKYPQKH 1429
+ KINY + +L+A T AS T Y+R E LGDA L +++++ L+ Q
Sbjct: 18 FEKKINYRFKNKAYLLQAFTHASYHYNTITDXYQRLEFLGDAILDYLITKHLYEDPRQHS 77
Query: 1430 EGQLTRMRQQMVSNLVLYQYALSKGLQSYIQA 1461
G LT +R +V+N + A+ Y +A
Sbjct: 78 PGVLTDLRSALVNNTIFASLAVKYDYHKYFKA 109
>pdb|2EB1|A Chain A, Crystal Structure Of The C-Terminal Rnase Iii Domain Of
Human Dicer
pdb|2EB1|B Chain B, Crystal Structure Of The C-Terminal Rnase Iii Domain Of
Human Dicer
pdb|2EB1|C Chain C, Crystal Structure Of The C-Terminal Rnase Iii Domain Of
Human Dicer
Length = 200
Score = 141 bits (355), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 76/177 (42%), Positives = 107/177 (60%), Gaps = 10/177 (5%)
Query: 1592 FHALEDALKIKFKDRGLLVEAITHASRPSSGVS-CYQRLEFVGDAVLDHLITKHLFFSYT 1650
F E + +FK++ L++A THAS + ++ CYQRLEF+GDA+LD+LITKHL+
Sbjct: 8 FENFEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPR 67
Query: 1651 NLPPGRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLE------- 1703
PG LTDLR+A VNN FA +AVK+ H + + S L I DFV+ LE
Sbjct: 68 QHSPGVLTDLRSALVNNTIFASLAVKYDYHKYFKAVSPELFHVIDDFVQFQLEKNEMQGM 127
Query: 1704 --ELLKPGFNSFGLGDCKAPKVLGDIVESIAGAIFLDSGRDTSVVWQVFQPLLDPMV 1758
EL + + D + PK +GDI ES+AGAI++DSG VWQV+ P++ P++
Sbjct: 128 DSELRRSEEDEEKEEDIEVPKAMGDIFESLAGAIYMDSGMSLETVWQVYYPMMRPLI 184
Score = 48.5 bits (114), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 47/92 (51%), Gaps = 4/92 (4%)
Query: 1374 LKDKINYPVP-ASKILEALTAASCQE---TFCYERAELLGDAYLKWVVSRFLFLKYPQKH 1429
+ KINY + +L+A T AS T CY+R E LGDA L +++++ L+ Q
Sbjct: 11 FEKKINYRFKNKAYLLQAFTHASYHYNTITDCYQRLEFLGDAILDYLITKHLYEDPRQHS 70
Query: 1430 EGQLTRMRQQMVSNLVLYQYALSKGLQSYIQA 1461
G LT +R +V+N + A+ Y +A
Sbjct: 71 PGVLTDLRSALVNNTIFASLAVKYDYHKYFKA 102
>pdb|4A2P|A Chain A, Structure Of Duck Rig-I Helicase Domain
pdb|4A36|A Chain A, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
pdb|4A36|B Chain B, Structure Of Duck Rig-I Helicase Domain Bound To 19-Mer
Dsrna And Atp Transition State Analogue
Length = 556
Score = 133 bits (335), Expect = 9e-31, Method: Compositional matrix adjust.
Identities = 137/560 (24%), Positives = 252/560 (45%), Gaps = 79/560 (14%)
Query: 299 MPEEQARPYQLDVLEQA-KKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFL 357
M ++AR YQ+++ + A KN + TG+GKT +++L+ ++ +K VFL
Sbjct: 3 METKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP-AGRKAKVVFL 61
Query: 358 VPKVPLVYQQAEVIR---EQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILL 414
KVP+ QQ V + E+ GY V G G++F + ++ + ++V+T QIL+
Sbjct: 62 ATKVPVYEQQKNVFKHHFERQGYSVQ---GISGENFSNVS-VEKVIEDSDIIVVTPQILV 117
Query: 415 NILRH-SIIKMEAINLLILDECHHAVKKHPYSLVMSEFYHT--TSKEKRPSVFGMTAS-- 469
N ++ + L+I DECH+ HPY+++M+ + S + P + G+TAS
Sbjct: 118 NSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVG 177
Query: 470 PVNLKGVSSQVDCAIKICNLESKLD-SVVCTIKDR-KELEKHVPMPSEVVVEYDKAASLW 527
N K + ++ IC+L S LD + T+++ +EL++ + P E D
Sbjct: 178 VGNAKNIEETIE---HICSLCSYLDIQAISTVRENIQELQRFMNKP-----EIDVRLVKR 229
Query: 528 SLHEQLKQMEVAVEEAAQSSSRRSKWQFMGARDAGAKEELRQVYGVSERTESDGAANLIQ 587
+H AA S+ S+ + + +R +Y V +++
Sbjct: 230 RIHNPF---------AAIISNLMSETEAL----------MRTIYSVDTLSQNSKK----- 265
Query: 588 KLRAINYALGELGQWCAYKVAQSFLTALQNDERANYQLDVKFQESYLSKVVSLLQCELV- 646
++ W + L L++ E +ES + + + + L
Sbjct: 266 -----DFGTQNYEHWIVVTQRKCRLLQLEDKE----------EESRICRALFICTEHLRK 310
Query: 647 --EGAVSKKDAKVVDSENGFVEGGTNEIEEGEL--LDSHVVSG-GEHVDVIIGAAVADGK 701
+ + +DA+++D+ + E TN ++ G L+ H+ + E +I + +
Sbjct: 311 YNDALIISEDARIIDALSYLTEFFTN-VKNGPYTELEQHLTAKFQEKEPELIALSKDETN 369
Query: 702 VTPKVQSLIKIL-LKYQHTEDFRAIIFVERVVAALVLPKVFAELPSLSFVKSASLIGHNN 760
PK++ L+ IL Y++ R ++F + L K E P L+++K L+G
Sbjct: 370 ENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGR 429
Query: 761 SQEMRTFQMQ------ETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAY 814
+ + + +D R LL+ATSVA+EG+DI QCN+V+ ++ + V
Sbjct: 430 RDQTTGMTLPSQKGVLDAFKTSKDNR--LLIATSVADEGIDIVQCNLVVLYEYSGNVTKM 487
Query: 815 IQSRGRARKPGSDYILMIER 834
IQ RGR R GS IL+ +
Sbjct: 488 IQVRGRGRAAGSKCILVTSK 507
>pdb|4A2Q|A Chain A, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|B Chain B, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|D Chain D, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
pdb|4A2Q|E Chain E, Structure Of Duck Rig-I Tandem Cards And Helicase Domain
Length = 797
Score = 133 bits (334), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 136/557 (24%), Positives = 251/557 (45%), Gaps = 79/557 (14%)
Query: 302 EQARPYQLDVLEQA-KKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLVPK 360
++AR YQ+++ + A KN + TG+GKT +++L+ ++ +K VFL K
Sbjct: 247 KKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP-AGRKAKVVFLATK 305
Query: 361 VPLVYQQAEVIR---EQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLNIL 417
VP+ QQ V + E+ GY V G G++F + ++ + ++V+T QIL+N
Sbjct: 306 VPVYEQQKNVFKHHFERQGYSVQ---GISGENFSNVS-VEKVIEDSDIIVVTPQILVNSF 361
Query: 418 RH-SIIKMEAINLLILDECHHAVKKHPYSLVMSEFYHT--TSKEKRPSVFGMTAS--PVN 472
++ + L+I DECH+ HPY+++M+ + S + P + G+TAS N
Sbjct: 362 EDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGN 421
Query: 473 LKGVSSQVDCAIKICNLESKLD-SVVCTIKDR-KELEKHVPMPSEVVVEYDKAASLWSLH 530
K + ++ IC+L S LD + T+++ +EL++ + P E D +H
Sbjct: 422 AKNIEETIE---HICSLCSYLDIQAISTVRENIQELQRFMNKP-----EIDVRLVKRRIH 473
Query: 531 EQLKQMEVAVEEAAQSSSRRSKWQFMGARDAGAKEELRQVYGVSERTESDGAANLIQKLR 590
AA S+ S+ + + +R +Y V +++
Sbjct: 474 NPF---------AAIISNLMSETEAL----------MRTIYSVDTLSQNSKK-------- 506
Query: 591 AINYALGELGQWCAYKVAQSFLTALQNDERANYQLDVKFQESYLSKVVSLLQCELV---E 647
++ W + L L++ E +ES + + + + L +
Sbjct: 507 --DFGTQNYEHWIVVTQRKCRLLQLEDKE----------EESRICRALFICTEHLRKYND 554
Query: 648 GAVSKKDAKVVDSENGFVEGGTNEIEEGEL--LDSHVVSG-GEHVDVIIGAAVADGKVTP 704
+ +DA+++D+ + E TN ++ G L+ H+ + E +I + + P
Sbjct: 555 ALIISEDARIIDALSYLTEFFTN-VKNGPYTELEQHLTAKFQEKEPELIALSKDETNENP 613
Query: 705 KVQSLIKIL-LKYQHTEDFRAIIFVERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQE 763
K++ L+ IL Y++ R ++F + L K E P L+++K L+G +
Sbjct: 614 KLEELVCILDDAYRYNPQTRTLLFAKTRALVSALKKCMEENPILNYIKPGVLMGRGRRDQ 673
Query: 764 MRTFQMQ------ETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQS 817
+ + +D R LL+ATSVA+EG+DI QCN+V+ ++ + V IQ
Sbjct: 674 TTGMTLPSQKGVLDAFKTSKDNR--LLIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQV 731
Query: 818 RGRARKPGSDYILMIER 834
RGR R GS IL+ +
Sbjct: 732 RGRGRAAGSKCILVTSK 748
>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
pdb|4GL2|B Chain B, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
Length = 699
Score = 93.2 bits (230), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 53/131 (40%), Positives = 80/131 (61%), Gaps = 6/131 (4%)
Query: 712 ILLKYQHTED-FRAIIFVERVVAALVLPKVFAELPSLS--FVKSASLIGHNNSQEMRTF- 767
I+ +Y TE+ R IIF + +A L + E + VK+ LIG +S E +
Sbjct: 390 IMEQYTRTEESARGIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMT 449
Query: 768 --QMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG 825
+ +E I+KFR G++ LL+AT+VAEEGLDI++CN+VIR+ L +A +Q+RGRAR
Sbjct: 450 QNEQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADE 509
Query: 826 SDYILMIERGN 836
S Y+L+ G+
Sbjct: 510 STYVLVAHSGS 520
Score = 67.0 bits (162), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 65/224 (29%), Positives = 107/224 (47%), Gaps = 28/224 (12%)
Query: 303 QARPYQLDVLEQA-KKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLVPKV 361
Q RPYQ++V + A + KN I L TG GKT +AV + + + ++ ++ + LV KV
Sbjct: 7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKV 66
Query: 362 PLVYQQAEVIREQTGYVVGHYCGEMGQDFWDAQ---RWQREFDTKQVLVMTAQILLNILR 418
LV Q + R++ + + +G D Q + + +++ TAQIL N L
Sbjct: 67 LLVEQ---LFRKEFQPFLKKWYRVIGLS-GDTQLKISFPEVVKSCDIIISTAQILENSLL 122
Query: 419 H------SIIKMEAINLLILDECHHAVKKHPYSLVMSEFYHTTSKEKR-----------P 461
+ + +++ +L+I+DECHH K+ Y+ +M + K R P
Sbjct: 123 NLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIPLP 182
Query: 462 SVFGMTASPVNLKGVSSQVDCAIKICNLESKLDSVVCTIKDRKE 505
+ G+TASP + G + Q I L + LD+ TIK KE
Sbjct: 183 QILGLTASP-GVGGATKQAKAEEHILKLCANLDAF--TIKTVKE 223
>pdb|3TBK|A Chain A, Mouse Rig-I Atpase Domain
Length = 555
Score = 89.4 bits (220), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 73/227 (32%), Positives = 112/227 (49%), Gaps = 22/227 (9%)
Query: 303 QARPYQLDVLEQAKK-KNTIAFLETGAGKTLIAVLLIRSICNDLQRQ---NKKMLAVFLV 358
+ R YQL++ AKK KNTI TG GKT +++L IC ++ +K VF
Sbjct: 4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLL----ICEHHLKKFPCGQKGKVVFFA 59
Query: 359 PKVPLVYQQAEVIR---EQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLN 415
++P+ QQA V E+ GY + G D+ Q + ++++T QIL+N
Sbjct: 60 NQIPVYEQQATVFSRYFERLGYNIASISGATS----DSVSVQHIIEDNDIIILTPQILVN 115
Query: 416 ILRH-SIIKMEAINLLILDECHHAVKKHPYSLVMSEFYHTTSKEKR---PSVFGMTASPV 471
L + +I + L I DECH+ K HPY+ + + E R P V G+TAS V
Sbjct: 116 NLNNGAIPSLSVFTLXIFDECHNTSKNHPYNQIXFRYLDHKLGESRDPLPQVVGLTAS-V 174
Query: 472 NLKGVSSQVDCAIKICNLESKLD-SVVCTIKDR-KELEKHVPMPSEV 516
+ + + IC L + LD SV+ T++D ELE+ V P ++
Sbjct: 175 GVGDAKTAEEAXQHICKLCAALDASVIATVRDNVAELEQVVYKPQKI 221
Score = 69.3 bits (168), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 47/139 (33%), Positives = 74/139 (53%), Gaps = 5/139 (3%)
Query: 704 PKVQSLIKILLKYQHTE-DFRAIIFVERVVAALVLPKVFAELPSLSFVKSASLIGH--NN 760
PK++ L +L + H + + + I+FV+ L K E P+LSF+K L G N
Sbjct: 371 PKLRDLYLVLQEEYHLKPETKTILFVKTRALVDALKKWIEENPALSFLKPGILTGRGRTN 430
Query: 761 SQEMRTFQMQETIAK-FR-DGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSR 818
T Q+ + + FR G +L+ATSVA+EG+DI +CN+VI ++ V+ IQ+R
Sbjct: 431 RATGXTLPAQKCVLEAFRASGDNNILIATSVADEGIDIAECNLVILYEYVGNVIKXIQTR 490
Query: 819 GRARKPGSDYILMIERGNL 837
GR R S L+ ++
Sbjct: 491 GRGRARDSKCFLLTSSADV 509
>pdb|4A2W|A Chain A, Structure Of Full-Length Duck Rig-I
pdb|4A2W|B Chain B, Structure Of Full-Length Duck Rig-I
Length = 936
Score = 86.3 bits (212), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 64/223 (28%), Positives = 117/223 (52%), Gaps = 19/223 (8%)
Query: 302 EQARPYQLDVLEQA-KKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLVPK 360
++AR YQ+++ + A KN + TG+GKT +++L+ ++ +K VFL K
Sbjct: 247 KKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP-AGRKAKVVFLATK 305
Query: 361 VPLVYQQAEVIR---EQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLNIL 417
VP+ QQ V + E+ GY V G G++F + ++ + ++V+T QIL+N
Sbjct: 306 VPVYEQQKNVFKHHFERQGYSVQ---GISGENFSNVS-VEKVIEDSDIIVVTPQILVNSF 361
Query: 418 RH-SIIKMEAINLLILDECHHAVKKHPYSLVMSEFYHT--TSKEKRPSVFGMTAS--PVN 472
++ + L+I DECH+ HPY+++M+ + S + P + G+TAS N
Sbjct: 362 EDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGVGN 421
Query: 473 LKGVSSQVDCAIKICNLESKLD-SVVCTIKDR-KELEKHVPMP 513
K + ++ IC+L S LD + T+++ +EL++ + P
Sbjct: 422 AKNIEETIE---HICSLCSYLDIQAISTVRENIQELQRFMNKP 461
Score = 76.3 bits (186), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 61/224 (27%), Positives = 109/224 (48%), Gaps = 16/224 (7%)
Query: 624 QLDVKFQESYLSKVVSLLQCELV---EGAVSKKDAKVVDSENGFVEGGTNEIEEGEL--L 678
QL+ K +ES + + + + L + + +DA+++D+ + E TN ++ G L
Sbjct: 528 QLEDKEEESRICRALFICTEHLRKYNDALIISEDARIIDALSYLTEFFTN-VKNGPYTEL 586
Query: 679 DSHVVSG-GEHVDVIIGAAVADGKVTPKVQSLIKILL-KYQHTEDFRAIIFVERVVAALV 736
+ H+ + E +I + + PK++ L+ IL Y++ R ++F +
Sbjct: 587 EQHLTAKFQEKEPELIALSKDETNENPKLEELVCILDDAYRYNPQTRTLLFAKTRALVSA 646
Query: 737 LPKVFAELPSLSFVKSASLIGHNNSQEMRTFQMQ------ETIAKFRDGRVTLLVATSVA 790
L K E P L+++K L+G + + + +D R LL+ATSVA
Sbjct: 647 LKKCMEENPILNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNR--LLIATSVA 704
Query: 791 EEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSDYILMIER 834
+EG+DI QCN+V+ ++ + V IQ RGR R GS IL+ +
Sbjct: 705 DEGIDIVQCNLVVLYEYSGNVTKMIQVRGRGRAAGSKCILVTSK 748
>pdb|3TMI|A Chain A, Structural Basis For Rna Recognition And Activation Of
Rig-I
Length = 695
Score = 84.7 bits (208), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 73/226 (32%), Positives = 115/226 (50%), Gaps = 22/226 (9%)
Query: 303 QARPYQLDV-LEQAKKKNTIAFLETGAGKTLIAVLLIRSIC-NDLQR--QNKKMLAVFLV 358
+ R YQL++ L K KNTI TG GKT +++L IC + L++ Q +K VF
Sbjct: 12 KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLL----ICEHHLKKFPQGQKGKVVFFA 67
Query: 359 PKVPLVYQQAEVIR---EQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLN 415
++P+ QQ V E+ GY V G ++ Q + ++++T QIL+N
Sbjct: 68 NQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQI----VENNDIIILTPQILVN 123
Query: 416 ILRHSII-KMEAINLLILDECHHAVKKHPYSLVMSEFYHTT---SKEKRPSVFGMTASPV 471
L+ I + L+I DECH+ K+HPY+++M + S P V G+TAS V
Sbjct: 124 NLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTAS-V 182
Query: 472 NLKGVSSQVDCAIKICNLESKLD-SVVCTIK-DRKELEKHVPMPSE 515
+ + + IC L + LD SV+ T+K + +ELE+ V P +
Sbjct: 183 GVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQK 228
Score = 67.8 bits (164), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 55/182 (30%), Positives = 82/182 (45%), Gaps = 12/182 (6%)
Query: 704 PKVQSLIKILLK-YQHTEDFRAIIFVERVVAALVLPKVFAELPSLSFVKSASLIGH--NN 760
PK++ L IL + Y + I+FV+ L P LSF+K L G N
Sbjct: 379 PKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTN 438
Query: 761 SQEMRTFQMQETI--AKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSR 818
T Q+ I A G +L+ATSVA+EG+DI QCN+VI ++ V+ IQ+R
Sbjct: 439 QNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTR 498
Query: 819 GRARKPGSDYILMIERGNL---SHATFLRNARNSEETLR----KEAIERTDLSHLKDTSR 871
GR R GS L+ + + ++ LR EA+ R + H++ +
Sbjct: 499 GRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEK 558
Query: 872 LI 873
I
Sbjct: 559 FI 560
>pdb|2YKG|A Chain A, Structural Insights Into Rna Recognition By Rig-I
Length = 696
Score = 83.2 bits (204), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 72/226 (31%), Positives = 114/226 (50%), Gaps = 22/226 (9%)
Query: 303 QARPYQLDV-LEQAKKKNTIAFLETGAGKTLIAVLLIRSIC-NDLQR--QNKKMLAVFLV 358
+ R YQL++ L K KNTI TG GKT +++L IC + L++ Q +K VF
Sbjct: 13 KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLL----ICEHHLKKFPQGQKGKVVFFA 68
Query: 359 PKVPLVYQQAEVIR---EQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLN 415
++P+ Q V E+ GY V G ++ Q + ++++T QIL+N
Sbjct: 69 NQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQI----VENNDIIILTPQILVN 124
Query: 416 ILRHSII-KMEAINLLILDECHHAVKKHPYSLVMSEFYHTT---SKEKRPSVFGMTASPV 471
L+ I + L+I DECH+ K+HPY+++M + S P V G+TAS V
Sbjct: 125 NLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTAS-V 183
Query: 472 NLKGVSSQVDCAIKICNLESKLD-SVVCTIK-DRKELEKHVPMPSE 515
+ + + IC L + LD SV+ T+K + +ELE+ V P +
Sbjct: 184 GVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQK 229
Score = 67.8 bits (164), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 55/182 (30%), Positives = 82/182 (45%), Gaps = 12/182 (6%)
Query: 704 PKVQSLIKILLK-YQHTEDFRAIIFVERVVAALVLPKVFAELPSLSFVKSASLIGH--NN 760
PK++ L IL + Y + I+FV+ L P LSF+K L G N
Sbjct: 380 PKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTN 439
Query: 761 SQEMRTFQMQETI--AKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSR 818
T Q+ I A G +L+ATSVA+EG+DI QCN+VI ++ V+ IQ+R
Sbjct: 440 QNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTR 499
Query: 819 GRARKPGSDYILMIERGNL---SHATFLRNARNSEETLR----KEAIERTDLSHLKDTSR 871
GR R GS L+ + + ++ LR EA+ R + H++ +
Sbjct: 500 GRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEK 559
Query: 872 LI 873
I
Sbjct: 560 FI 561
>pdb|4AY2|A Chain A, Capturing 5' Tri-Phosphorylated Rna Duplex By Rig-I
Length = 687
Score = 82.8 bits (203), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 72/226 (31%), Positives = 114/226 (50%), Gaps = 22/226 (9%)
Query: 303 QARPYQLDV-LEQAKKKNTIAFLETGAGKTLIAVLLIRSIC-NDLQR--QNKKMLAVFLV 358
+ R YQL++ L K KNTI TG GKT +++L IC + L++ Q +K VF
Sbjct: 4 KPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLL----ICEHHLKKFPQGQKGKVVFFA 59
Query: 359 PKVPLVYQQAEVIR---EQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLN 415
++P+ Q V E+ GY V G ++ Q + ++++T QIL+N
Sbjct: 60 NQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQI----VENNDIIILTPQILVN 115
Query: 416 ILRHSII-KMEAINLLILDECHHAVKKHPYSLVMSEFYHTT---SKEKRPSVFGMTASPV 471
L+ I + L+I DECH+ K+HPY+++M + S P V G+TAS V
Sbjct: 116 NLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTAS-V 174
Query: 472 NLKGVSSQVDCAIKICNLESKLD-SVVCTIK-DRKELEKHVPMPSE 515
+ + + IC L + LD SV+ T+K + +ELE+ V P +
Sbjct: 175 GVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQK 220
Score = 67.8 bits (164), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 55/182 (30%), Positives = 82/182 (45%), Gaps = 12/182 (6%)
Query: 704 PKVQSLIKILLK-YQHTEDFRAIIFVERVVAALVLPKVFAELPSLSFVKSASLIGH--NN 760
PK++ L IL + Y + I+FV+ L P LSF+K L G N
Sbjct: 371 PKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTN 430
Query: 761 SQEMRTFQMQETI--AKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSR 818
T Q+ I A G +L+ATSVA+EG+DI QCN+VI ++ V+ IQ+R
Sbjct: 431 QNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTR 490
Query: 819 GRARKPGSDYILMIERGNL---SHATFLRNARNSEETLR----KEAIERTDLSHLKDTSR 871
GR R GS L+ + + ++ LR EA+ R + H++ +
Sbjct: 491 GRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEK 550
Query: 872 LI 873
I
Sbjct: 551 FI 552
>pdb|3N3W|A Chain A, 2.2 Angstrom Resolution Crystal Structure Of Nuclease Domain
Ribonuclase Iii (Rnc) From Campylobacter Jejuni
pdb|3N3W|B Chain B, 2.2 Angstrom Resolution Crystal Structure Of Nuclease Domain
Ribonuclase Iii (Rnc) From Campylobacter Jejuni
Length = 248
Score = 79.3 bits (194), Expect = 2e-14, Method: Composition-based stats.
Identities = 72/240 (30%), Positives = 120/240 (50%), Gaps = 36/240 (15%)
Query: 1591 DFHALEDALKIKFKDRGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITKHLFFSYT 1650
+ LE +L +FKD+ LL+ A+TH S S + +RLEF+GDAVLD ++ ++LF +
Sbjct: 27 NIEKLEQSLTYEFKDKNLLIHALTHKSFKKSYNN--ERLEFLGDAVLDLVVGEYLFHKFA 84
Query: 1651 NLPPGRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFV-KEVLEELLKPG 1709
G L+ LRAA VN ++FA++A L DF+ V EE
Sbjct: 85 KDAEGDLSKLRAALVNEKSFAKIANSLNLG---------------DFILMSVAEE----- 124
Query: 1710 FNSFGLGDCKAPKVLGDIVESIAGAIFLDSGRD--TSVVWQVFQPLLDPMVTPETLPMHP 1767
G + P +L D +E+I GAI L++G + ++ ++ + P + + L
Sbjct: 125 ----NNGGKEKPSILSDALEAIIGAIHLEAGFEFAKTIALRLIEKNF-PQIDAKILIKDY 179
Query: 1768 VRELQERCQQQ-AEGLEYKASRS---GNLATVEV--YIDGVQVGVAQNPQKKMAQKLAAR 1821
+LQE Q + + +Y+ R+ +L E+ +DG ++ A KK AQ++AA+
Sbjct: 180 KTKLQEITQGKIGQTPQYETVRAFGPDHLKQFEIALMLDGKELARAIAGSKKEAQQMAAK 239
Score = 49.3 bits (116), Expect = 2e-05, Method: Composition-based stats.
Identities = 32/100 (32%), Positives = 53/100 (53%), Gaps = 9/100 (9%)
Query: 1362 MRRVESM--LLAIQLKDKINYPVPASKILEALTAASCQETFCYERAELLGDAYLKWVVSR 1419
M+ +E + L + KDK + ++ ALT S ++++ ER E LGDA L VV
Sbjct: 25 MKNIEKLEQSLTYEFKDK-------NLLIHALTHKSFKKSYNNERLEFLGDAVLDLVVGE 77
Query: 1420 FLFLKYPQKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYI 1459
+LF K+ + EG L+++R +V+ + A S L +I
Sbjct: 78 YLFHKFAKDAEGDLSKLRAALVNEKSFAKIANSLNLGDFI 117
>pdb|3O2R|A Chain A, Structural Flexibility In Region Involved In Dimer Formation
Of Nuclease Domain Of Ribonuclase Iii (Rnc) From
Campylobacter Jejuni
pdb|3O2R|C Chain C, Structural Flexibility In Region Involved In Dimer Formation
Of Nuclease Domain Of Ribonuclase Iii (Rnc) From
Campylobacter Jejuni
Length = 170
Score = 75.5 bits (184), Expect = 3e-13, Method: Composition-based stats.
Identities = 53/151 (35%), Positives = 83/151 (54%), Gaps = 27/151 (17%)
Query: 1591 DFHALEDALKIKFKDRGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITKHLFFSYT 1650
+ LE +L +FKD+ LL+ A+TH S S + +RLEF+GDAVLD ++ ++LF +
Sbjct: 27 NIEKLEQSLTYEFKDKNLLIHALTHKSFKKSYNN--ERLEFLGDAVLDLVVGEYLFHKFA 84
Query: 1651 NLPPGRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFV-KEVLEELLKPG 1709
G L+ LRAA VN ++FA++A ++L+ + DF+ V EE
Sbjct: 85 KDAEGDLSKLRAALVNEKSFAKIA-------------NSLN--LGDFILMSVAEE----- 124
Query: 1710 FNSFGLGDCKAPKVLGDIVESIAGAIFLDSG 1740
G + P +L D +E+I GAI L++G
Sbjct: 125 ----NNGGKEKPSILSDALEAIIGAIHLEAG 151
Score = 49.7 bits (117), Expect = 2e-05, Method: Composition-based stats.
Identities = 32/100 (32%), Positives = 53/100 (53%), Gaps = 9/100 (9%)
Query: 1362 MRRVESM--LLAIQLKDKINYPVPASKILEALTAASCQETFCYERAELLGDAYLKWVVSR 1419
M+ +E + L + KDK + ++ ALT S ++++ ER E LGDA L VV
Sbjct: 25 MKNIEKLEQSLTYEFKDK-------NLLIHALTHKSFKKSYNNERLEFLGDAVLDLVVGE 77
Query: 1420 FLFLKYPQKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYI 1459
+LF K+ + EG L+++R +V+ + A S L +I
Sbjct: 78 YLFHKFAKDAEGDLSKLRAALVNEKSFAKIANSLNLGDFI 117
>pdb|3O2R|B Chain B, Structural Flexibility In Region Involved In Dimer Formation
Of Nuclease Domain Of Ribonuclase Iii (Rnc) From
Campylobacter Jejuni
pdb|3O2R|D Chain D, Structural Flexibility In Region Involved In Dimer Formation
Of Nuclease Domain Of Ribonuclase Iii (Rnc) From
Campylobacter Jejuni
Length = 144
Score = 74.7 bits (182), Expect = 5e-13, Method: Composition-based stats.
Identities = 52/151 (34%), Positives = 82/151 (54%), Gaps = 26/151 (17%)
Query: 1591 DFHALEDALKIKFKDRGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITKHLFFSYT 1650
+ LE +L +FKD+ LL+ A+TH S + +RLEF+GDAVLD ++ ++LF +
Sbjct: 1 NIEKLEQSLTYEFKDKNLLIHALTHKSFXKKSYN-NERLEFLGDAVLDLVVGEYLFHKFA 59
Query: 1651 NLPPGRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFV-KEVLEELLKPG 1709
G L+ LRAA VN ++FA++A ++L+ + DF+ V EE
Sbjct: 60 KDAEGDLSKLRAALVNEKSFAKIA-------------NSLN--LGDFILMSVAEE----- 99
Query: 1710 FNSFGLGDCKAPKVLGDIVESIAGAIFLDSG 1740
G + P +L D +E+I GAI L++G
Sbjct: 100 ----NNGGKEKPSILSDALEAIIGAIHLEAG 126
Score = 44.7 bits (104), Expect = 6e-04, Method: Composition-based stats.
Identities = 30/91 (32%), Positives = 48/91 (52%), Gaps = 8/91 (8%)
Query: 1370 LAIQLKDKINYPVPASKILEALTAAS-CQETFCYERAELLGDAYLKWVVSRFLFLKYPQK 1428
L + KDK + ++ ALT S ++++ ER E LGDA L VV +LF K+ +
Sbjct: 9 LTYEFKDK-------NLLIHALTHKSFXKKSYNNERLEFLGDAVLDLVVGEYLFHKFAKD 61
Query: 1429 HEGQLTRMRQQMVSNLVLYQYALSKGLQSYI 1459
EG L+++R +V+ + A S L +I
Sbjct: 62 AEGDLSKLRAALVNEKSFAKIANSLNLGDFI 92
>pdb|2KOU|A Chain A, Dicer Like Protein
Length = 102
Score = 70.9 bits (172), Expect = 7e-12, Method: Composition-based stats.
Identities = 35/105 (33%), Positives = 57/105 (54%), Gaps = 3/105 (2%)
Query: 892 VSLNSAVGLIHFYCSQLPSDRYSILRPEFIMERHEKPGGPTEYSCKLQLPCNAPFEKLEG 951
+S S++ +++ YCS+LP D + +PEF + ++ GG C++ LP NAP ++E
Sbjct: 1 ISGGSSISMMYKYCSRLPHDEFFQPKPEFQFKPVDEFGGTI---CRITLPANAPISEIES 57
Query: 952 PVCSSMRLAQQAVCLAACKKLHEMGAFTDMLLPDKGSGEQQEKVD 996
+ S A++ CL A +LH +G D LLPD + E D
Sbjct: 58 SLLPSTEAAKKDACLKAVHELHNLGVLNDFLLPDSKDEIEDELSD 102
>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 = 69.3 bits (168), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 54/170 (31%), Positives = 80/170 (47%), Gaps = 14/170 (8%)
Query: 303 QARPYQLDVLEQAKKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLVPKVP 362
Q R YQ + + K+ N + L TG GKTLIA+++ L + K+L L P P
Sbjct: 9 QPRIYQEVIYAKCKETNCLIVLPTGLGKTLIAMMIAEY---RLTKYGGKVL--MLAPTKP 63
Query: 363 LVYQQAEVIREQTGYVVGHYCGEMGQDFWD--AQRWQREFDTKQVLVMTAQILLNILRHS 420
LV Q AE R G+ + ++ W R +V+V T Q + N L
Sbjct: 64 LVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKAWAR----AKVIVATPQTIENDLLAG 119
Query: 421 IIKMEAINLLILDECHHAVKKHPYSLVMSEFYHTTSKEKRPSVFGMTASP 470
I +E ++L++ DE H AV + Y + E+ + K P V G+TASP
Sbjct: 120 RISLEDVSLIVFDEAHRAVGNYAYVFIAREY---KRQAKNPLVIGLTASP 166
Score = 48.5 bits (114), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 39/134 (29%), Positives = 67/134 (50%), Gaps = 10/134 (7%)
Query: 704 PKVQSLIKILL-KYQHTEDFRAIIFVERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQ 762
PK+ L +I+ + Q ++ + I+F A K+ EL +K+ +G + +
Sbjct: 343 PKMDKLKEIIREQLQRKQNSKIIVFTNYRETA---KKIVNELVK-DGIKAKRFVGQASKE 398
Query: 763 EMRTFQMQE---TIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRG 819
R +E + +F G +LVATSV EEGLD+ + ++V+ ++ + + IQ RG
Sbjct: 399 NDRGLSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRG 458
Query: 820 RARK--PGSDYILM 831
R + PG ILM
Sbjct: 459 RTGRHMPGRVIILM 472
>pdb|4I1S|A Chain A, Melanoma Differentiation Associated Protein-5 Helicase
Domain Complex With Inhibitor Non-structural Protein V
Length = 243
Score = 68.6 bits (166), Expect = 3e-11, Method: Composition-based stats.
Identities = 42/97 (43%), Positives = 59/97 (60%), Gaps = 13/97 (13%)
Query: 720 EDFRAIIFVERVVAALVLP------KVFAELPSLSFVKSASLIGHNNSQEMRTF---QMQ 770
E R IIF + +A L K FAE+ VK+ LIG +S E + + +
Sbjct: 149 ESARGIIFTKTRQSAYALSQWITDNKKFAEVG----VKAHHLIGAGHSSEFKPXTQNEQR 204
Query: 771 ETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDL 807
E I+KFR G++ LL+AT+VAEEGLDI++CN+VIR+ L
Sbjct: 205 EVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGL 241
>pdb|2A11|A Chain A, Crystal Structure Of Nuclease Domain Of Ribonuclase Iii From
Mycobacterium Tuberculosis
Length = 242
Score = 66.2 bits (160), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 56/169 (33%), Positives = 76/169 (44%), Gaps = 25/169 (14%)
Query: 1595 LEDALKIKFKDRGLLVEAITHASRP--SSGVSCYQRLEFVGDAVLDHLITKHLFFSYTNL 1652
L DAL + D LL A+TH S + G+ +RLEF+GDAVL IT LF + +
Sbjct: 10 LLDALGVDLPDE-LLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHPDR 68
Query: 1653 PPGRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLEELLKPGFNS 1712
G L LRA+ VN + A VA R E L + G
Sbjct: 69 SEGDLAKLRASVVNTQALADVA--------------------RRLCAEGLGVHVLLGRGE 108
Query: 1713 FGLGDCKAPKVLGDIVESIAGAIFLDSGRDTS--VVWQVFQPLLDPMVT 1759
G +L D +ES+ GAI+L G + + V+ ++F PLLD T
Sbjct: 109 ANTGGADKSSILADGMESLLGAIYLQHGMEKAREVILRLFGPLLDAAPT 157
Score = 40.8 bits (94), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 8/70 (11%)
Query: 1389 EALTAASCQETFCYE--------RAELLGDAYLKWVVSRFLFLKYPQKHEGQLTRMRQQM 1440
E L+ A ++ YE R E LGDA L ++ LF ++P + EG L ++R +
Sbjct: 21 ELLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHPDRSEGDLAKLRASV 80
Query: 1441 VSNLVLYQYA 1450
V+ L A
Sbjct: 81 VNTQALADVA 90
>pdb|3B6E|A Chain A, Crystal Structure Of Human Dech-Box Rna Helicase Mda5
(Melanoma Differentiation-Associated Protein 5),
Dech-Domain
Length = 216
Score = 65.5 bits (158), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 55/191 (28%), Positives = 94/191 (49%), Gaps = 25/191 (13%)
Query: 300 PEEQARPYQLDVLEQA-KKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLV 358
PE Q RPYQ++V + A + KN I L TG+GKT +AV + + + ++ ++ + LV
Sbjct: 30 PELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLV 89
Query: 359 PKVPLVYQQAEVIREQTGYVVGHYCGEMGQDFWDAQ---RWQREFDTKQVLVMTAQILLN 415
KV LV Q + R++ + + +G D Q + + +++ TAQIL N
Sbjct: 90 NKVLLVEQ---LFRKEFQPFLKKWYRVIGLS-GDTQLKISFPEVVKSCDIIISTAQILEN 145
Query: 416 ILRH------SIIKMEAINLLILDECHHAVKKHPYSLVMSEFYHTTSKEKR--------- 460
L + + +++ +L+I+DECHH K+ Y+ +M + K R
Sbjct: 146 SLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVI 205
Query: 461 --PSVFGMTAS 469
P + G+TAS
Sbjct: 206 PLPQILGLTAS 216
>pdb|1JFZ|A Chain A, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|B Chain B, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|C Chain C, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1JFZ|D Chain D, Crystal Structure Of Mn(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.10
Angstrom Resolution
pdb|1RC5|A Chain A, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
pdb|1RC5|B Chain B, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
pdb|1RC5|C Chain C, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
pdb|1RC5|D Chain D, Crystal Structure Of Mg(Ii)-Complex Of Rnase Iii
Endonuclease Domain From Aquifex Aeolicus At 2.30
Angstrom Resolution
Length = 154
Score = 62.4 bits (150), Expect = 2e-09, Method: Composition-based stats.
Identities = 46/160 (28%), Positives = 73/160 (45%), Gaps = 31/160 (19%)
Query: 1595 LEDALKIKFKDRGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITKHLFFSYTNLPP 1654
LE L FKD+ LL +A+TH S S Y+ LEF+GDA+++ I L N
Sbjct: 8 LEKKLGYTFKDKSLLEKALTHVSY--SKKEHYETLEFLGDALVNFFIVDLLVQYSPNKRE 65
Query: 1655 GRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLEELLKPGFNSFG 1714
G L+ L+A ++ E F +A K +LH +R ++ I
Sbjct: 66 GFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI-------------------- 105
Query: 1715 LGDCKAPKVLGDIVESIAGAIFLDSGRDTSVVWQVFQPLL 1754
+GD+ E++ A+++DSGRD + ++F L
Sbjct: 106 ---------IGDVFEALWAAVYIDSGRDANFTRELFYKLF 136
Score = 40.8 bits (94), Expect = 0.007, Method: Composition-based stats.
Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 1/97 (1%)
Query: 1368 MLLAIQLKDKINYPVPASKILE-ALTAASCQETFCYERAELLGDAYLKWVVSRFLFLKYP 1426
M + QL+ K+ Y +LE ALT S + YE E LGDA + + + L P
Sbjct: 2 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSP 61
Query: 1427 QKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYIQADR 1463
K EG L+ ++ ++S A L +I+ R
Sbjct: 62 NKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKR 98
>pdb|1I4S|A Chain A, Crystal Structure Of Rnase Iii Endonuclease Domain From
Aquifex Aeolicus At 2.15 Angstrom Resolution
pdb|1I4S|B Chain B, Crystal Structure Of Rnase Iii Endonuclease Domain From
Aquifex Aeolicus At 2.15 Angstrom Resolution
Length = 147
Score = 62.4 bits (150), Expect = 3e-09, Method: Composition-based stats.
Identities = 46/160 (28%), Positives = 73/160 (45%), Gaps = 31/160 (19%)
Query: 1595 LEDALKIKFKDRGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITKHLFFSYTNLPP 1654
LE L FKD+ LL +A+TH S S Y+ LEF+GDA+++ I L N
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSY--SKKEHYETLEFLGDALVNFFIVDLLVQYSPNKRE 64
Query: 1655 GRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLEELLKPGFNSFG 1714
G L+ L+A ++ E F +A K +LH +R ++ I
Sbjct: 65 GFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI-------------------- 104
Query: 1715 LGDCKAPKVLGDIVESIAGAIFLDSGRDTSVVWQVFQPLL 1754
+GD+ E++ A+++DSGRD + ++F L
Sbjct: 105 ---------IGDVFEALWAAVYIDSGRDANFTRELFYKLF 135
Score = 40.8 bits (94), Expect = 0.007, Method: Composition-based stats.
Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 1/97 (1%)
Query: 1368 MLLAIQLKDKINYPVPASKILE-ALTAASCQETFCYERAELLGDAYLKWVVSRFLFLKYP 1426
M + QL+ K+ Y +LE ALT S + YE E LGDA + + + L P
Sbjct: 1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSP 60
Query: 1427 QKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYIQADR 1463
K EG L+ ++ ++S A L +I+ R
Sbjct: 61 NKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKR 97
>pdb|1YYK|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double-Stranded Rna At 2.5-Angstrom
Resolution
pdb|1YYK|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double-Stranded Rna At 2.5-Angstrom
Resolution
pdb|1YYW|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|C Chain C, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|1YYW|D Chain D, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Double Stranded Rna At 2.8-Angstrom
Resolution
pdb|2NUE|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.9-Angstrom Resolution
pdb|2NUE|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.9-Angstrom Resolution
pdb|2NUF|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.5-Angstrom Resolution
pdb|2NUF|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 2.5-Angstrom Resolution
pdb|2NUG|A Chain A, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 1.7-Angstrom Resolution
pdb|2NUG|B Chain B, Crystal Structure Of Rnase Iii From Aquifex Aeolicus
Complexed With Ds-Rna At 1.7-Angstrom Resolution
Length = 221
Score = 60.5 bits (145), Expect = 9e-09, Method: Composition-based stats.
Identities = 46/160 (28%), Positives = 73/160 (45%), Gaps = 31/160 (19%)
Query: 1595 LEDALKIKFKDRGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITKHLFFSYTNLPP 1654
LE L FKD+ LL +A+TH S S Y+ LEF+GDA+++ I L N
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSY--SKKEHYETLEFLGDALVNFFIVDLLVQYSPNKRE 64
Query: 1655 GRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLEELLKPGFNSFG 1714
G L+ L+A ++ E F +A K +LH +R ++ I
Sbjct: 65 GFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI-------------------- 104
Query: 1715 LGDCKAPKVLGDIVESIAGAIFLDSGRDTSVVWQVFQPLL 1754
+GD+ E++ A+++DSGRD + ++F L
Sbjct: 105 ---------IGDVFEALWAAVYIDSGRDANFTRELFYKLF 135
Score = 40.0 bits (92), Expect = 0.013, Method: Composition-based stats.
Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 1/97 (1%)
Query: 1368 MLLAIQLKDKINYPVPASKILE-ALTAASCQETFCYERAELLGDAYLKWVVSRFLFLKYP 1426
M + QL+ K+ Y +LE ALT S + YE E LGDA + + + L P
Sbjct: 1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSP 60
Query: 1427 QKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYIQADR 1463
K EG L+ ++ ++S A L +I+ R
Sbjct: 61 NKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKR 97
>pdb|1YZ9|A Chain A, Crystal Structure Of Rnase Iii Mutant E110q From Aquifex
Aeolicus Complexed With Double Stranded Rna At 2.1-
Angstrom Resolution
pdb|1YZ9|B Chain B, Crystal Structure Of Rnase Iii Mutant E110q From Aquifex
Aeolicus Complexed With Double Stranded Rna At 2.1-
Angstrom Resolution
Length = 221
Score = 59.3 bits (142), Expect = 2e-08, Method: Composition-based stats.
Identities = 45/160 (28%), Positives = 73/160 (45%), Gaps = 31/160 (19%)
Query: 1595 LEDALKIKFKDRGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITKHLFFSYTNLPP 1654
LE L FKD+ LL +A+TH S S Y+ LEF+GDA+++ I L N
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSY--SKKEHYETLEFLGDALVNFFIVDLLVQYSPNKRE 64
Query: 1655 GRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLEELLKPGFNSFG 1714
G L+ L+A ++ E F +A K +LH +R ++ I
Sbjct: 65 GFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI-------------------- 104
Query: 1715 LGDCKAPKVLGDIVESIAGAIFLDSGRDTSVVWQVFQPLL 1754
+GD+ +++ A+++DSGRD + ++F L
Sbjct: 105 ---------IGDVFQALWAAVYIDSGRDANFTRELFYKLF 135
Score = 40.0 bits (92), Expect = 0.013, Method: Composition-based stats.
Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 1/97 (1%)
Query: 1368 MLLAIQLKDKINYPVPASKILE-ALTAASCQETFCYERAELLGDAYLKWVVSRFLFLKYP 1426
M + QL+ K+ Y +LE ALT S + YE E LGDA + + + L P
Sbjct: 1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSP 60
Query: 1427 QKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYIQADR 1463
K EG L+ ++ ++S A L +I+ R
Sbjct: 61 NKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKR 97
>pdb|1RC7|A Chain A, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex
Aeolicus Complexed With Ds-Rna At 2.15 Angstrom
Resolution
Length = 220
Score = 58.9 bits (141), Expect = 2e-08, Method: Composition-based stats.
Identities = 45/160 (28%), Positives = 73/160 (45%), Gaps = 31/160 (19%)
Query: 1595 LEDALKIKFKDRGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITKHLFFSYTNLPP 1654
LE L FKD+ LL +A+TH S S Y+ LEF+GDA+++ I L N
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSY--SKKEHYETLEFLGDALVNFFIVDLLVQYSPNKRE 64
Query: 1655 GRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLEELLKPGFNSFG 1714
G L+ L+A ++ E F +A K +LH +R ++ I
Sbjct: 65 GFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI-------------------- 104
Query: 1715 LGDCKAPKVLGDIVESIAGAIFLDSGRDTSVVWQVFQPLL 1754
+GD+ +++ A+++DSGRD + ++F L
Sbjct: 105 ---------IGDVFKALWAAVYIDSGRDANFTRELFYKLF 135
Score = 40.0 bits (92), Expect = 0.013, Method: Composition-based stats.
Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 1/97 (1%)
Query: 1368 MLLAIQLKDKINYPVPASKILE-ALTAASCQETFCYERAELLGDAYLKWVVSRFLFLKYP 1426
M + QL+ K+ Y +LE ALT S + YE E LGDA + + + L P
Sbjct: 1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSP 60
Query: 1427 QKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYIQADR 1463
K EG L+ ++ ++S A L +I+ R
Sbjct: 61 NKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKR 97
>pdb|1YYO|A Chain A, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex
Aeolicus Complexed With Double-stranded Rna At 2.9-
Angstrom Resolution
pdb|1YYO|B Chain B, Crystal Structure Of Rnase Iii Mutant E110k From Aquifex
Aeolicus Complexed With Double-stranded Rna At 2.9-
Angstrom Resolution
Length = 221
Score = 58.9 bits (141), Expect = 3e-08, Method: Composition-based stats.
Identities = 45/160 (28%), Positives = 73/160 (45%), Gaps = 31/160 (19%)
Query: 1595 LEDALKIKFKDRGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITKHLFFSYTNLPP 1654
LE L FKD+ LL +A+TH S S Y+ LEF+GDA+++ I L N
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSY--SKKEHYETLEFLGDALVNFFIVDLLVQYSPNKRE 64
Query: 1655 GRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLEELLKPGFNSFG 1714
G L+ L+A ++ E F +A K +LH +R ++ I
Sbjct: 65 GFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI-------------------- 104
Query: 1715 LGDCKAPKVLGDIVESIAGAIFLDSGRDTSVVWQVFQPLL 1754
+GD+ +++ A+++DSGRD + ++F L
Sbjct: 105 ---------IGDVFKALWAAVYIDSGRDANFTRELFYKLF 135
Score = 40.0 bits (92), Expect = 0.013, Method: Composition-based stats.
Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 1/97 (1%)
Query: 1368 MLLAIQLKDKINYPVPASKILE-ALTAASCQETFCYERAELLGDAYLKWVVSRFLFLKYP 1426
M + QL+ K+ Y +LE ALT S + YE E LGDA + + + L P
Sbjct: 1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSP 60
Query: 1427 QKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYIQADR 1463
K EG L+ ++ ++S A L +I+ R
Sbjct: 61 NKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKR 97
>pdb|2EZ6|A Chain A, Crystal Structure Of Aquifex Aeolicus Rnase Iii (d44n)
Complexed With Product Of Double-stranded Rna Processing
pdb|2EZ6|B Chain B, Crystal Structure Of Aquifex Aeolicus Rnase Iii (d44n)
Complexed With Product Of Double-stranded Rna Processing
Length = 221
Score = 58.9 bits (141), Expect = 3e-08, Method: Composition-based stats.
Identities = 45/160 (28%), Positives = 73/160 (45%), Gaps = 31/160 (19%)
Query: 1595 LEDALKIKFKDRGLLVEAITHASRPSSGVSCYQRLEFVGDAVLDHLITKHLFFSYTNLPP 1654
LE L FKD+ LL +A+TH S S Y+ LEF+G+A+++ I L N
Sbjct: 7 LEKKLGYTFKDKSLLEKALTHVSY--SKKEHYETLEFLGNALVNFFIVDLLVQYSPNKRE 64
Query: 1655 GRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLEELLKPGFNSFG 1714
G L+ L+A ++ E F +A K +LH +R ++ I
Sbjct: 65 GFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETI-------------------- 104
Query: 1715 LGDCKAPKVLGDIVESIAGAIFLDSGRDTSVVWQVFQPLL 1754
+GD+ E++ A+++DSGRD + ++F L
Sbjct: 105 ---------IGDVFEALWAAVYIDSGRDANFTRELFYKLF 135
Score = 38.1 bits (87), Expect = 0.046, Method: Composition-based stats.
Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 1/97 (1%)
Query: 1368 MLLAIQLKDKINYPVPASKILE-ALTAASCQETFCYERAELLGDAYLKWVVSRFLFLKYP 1426
M + QL+ K+ Y +LE ALT S + YE E LG+A + + + L P
Sbjct: 1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGNALVNFFIVDLLVQYSP 60
Query: 1427 QKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYIQADR 1463
K EG L+ ++ ++S A L +I+ R
Sbjct: 61 NKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKR 97
>pdb|1O0W|A Chain A, Crystal Structure Of Ribonuclease Iii (Tm1102) From
Thermotoga Maritima At 2.0 A Resolution
pdb|1O0W|B Chain B, Crystal Structure Of Ribonuclease Iii (Tm1102) From
Thermotoga Maritima At 2.0 A Resolution
Length = 252
Score = 58.5 bits (140), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 62/236 (26%), Positives = 99/236 (41%), Gaps = 39/236 (16%)
Query: 1601 IKFKDRGLLVEAITHASRPSS-------GVSCYQRLEFVGDAVLDHLITKHLFFSYTNLP 1653
I FK+ LL A+ H+S + V ++LEF+GDAVL+ + + L+ Y
Sbjct: 30 INFKNEELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEAE 89
Query: 1654 PGRLTDLRAAAVNNENFARVAVKHKLHVHLRHGSSALDRQIRDFVKEVLEELLKPGFNSF 1713
G L +++AA + E A V+ K L L G RD
Sbjct: 90 VGDLARVKSAAASEEVLAMVSRKMNLGKFLFLGKGEEKTGGRD----------------- 132
Query: 1714 GLGDCKAPKVLGDIVESIAGAIFLDSGRD--TSVVWQVFQPLLDPMVTPETLPMHPVREL 1771
+L D E++ AI+LD G + + Q F+ ++ ++ E L + L
Sbjct: 133 ------RDSILADAFEALLAAIYLDQGYEKIKELFEQEFEFYIEKIMKGEMLFDYKTA-L 185
Query: 1772 QERCQQQAE-GLEYKASRS-----GNLATVEVYIDGVQVGVAQNPQKKMAQKLAAR 1821
QE Q + + EY R+ + VEV ++G + + KK A+K AAR
Sbjct: 186 QEIVQSEHKVPPEYILVRTEKNDGDRIFVVEVRVNGKTIATGKGRTKKEAEKEAAR 241
Score = 36.6 bits (83), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 1403 ERAELLGDAYLKWVVSRFLFLKYPQKHEGQLTRMRQQMVSNLVL 1446
E+ E LGDA L+ V L+ KYP+ G L R++ S VL
Sbjct: 63 EKLEFLGDAVLELFVCEILYKKYPEAEVGDLARVKSAAASEEVL 106
>pdb|2JGN|A Chain A, Ddx3 Helicase Domain
pdb|2JGN|B Chain B, Ddx3 Helicase Domain
pdb|2JGN|C Chain C, Ddx3 Helicase Domain
Length = 185
Score = 50.4 bits (119), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 39/79 (49%), Gaps = 10/79 (12%)
Query: 770 QETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSDYI 829
+E + +FR G+ +LVAT+VA GLDI VI FDL + Y+ GR +
Sbjct: 86 EEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV----- 140
Query: 830 LMIERGNLSHATFLRNARN 848
GNL AT N RN
Sbjct: 141 -----GNLGLATSFFNERN 154
>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x
Length = 417
Score = 50.1 bits (118), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 39/79 (49%), Gaps = 10/79 (12%)
Query: 770 QETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSDYI 829
+E + +FR G+ +LVAT+VA GLDI VI FDL + Y+ GR +
Sbjct: 316 EEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRV----- 370
Query: 830 LMIERGNLSHATFLRNARN 848
GNL AT N RN
Sbjct: 371 -----GNLGLATSFFNERN 384
>pdb|3RV0|A Chain A, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
pdb|3RV0|B Chain B, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
pdb|3RV0|C Chain C, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
pdb|3RV0|D Chain D, Crystal Structure Of K. Polysporus Dcr1 Without The
C-Terminal Dsrbd
Length = 341
Score = 48.1 bits (113), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 51/104 (49%), Gaps = 13/104 (12%)
Query: 1378 INYPVPASKILEALTAA------------SCQET-FCYERAELLGDAYLKWVVSRFLFLK 1424
I YPV + LE L Q+T ER E LGD++L +VS ++ +
Sbjct: 92 IKYPVVYDENLENLAFMHKSFPNMNAHLNDAQKTQLSNERLEFLGDSWLGALVSYIVYTR 151
Query: 1425 YPQKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYIQADRFAPSR 1468
+P +EG L++M++ +V+N L+ ++ +Q + P+R
Sbjct: 152 FPSANEGMLSQMKESIVNNNNLFDWSTKLNFTKRLQGNIATPTR 195
Score = 35.4 bits (80), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 50/207 (24%), Positives = 80/207 (38%), Gaps = 38/207 (18%)
Query: 1627 QRLEFVGDAVLDHLITKHLFFSYTNLPP---GRLTDLRAAAVNNENFARVAVKHKLHVHL 1683
+RLEF+GD+ L L++ + YT P G L+ ++ + VNN N + K L
Sbjct: 130 ERLEFLGDSWLGALVS---YIVYTRFPSANEGMLSQMKESIVNNNNLFDWSTKLNFTKRL 186
Query: 1684 RHGSSALDRQIRDFVKEVLEELLKPGFNSFGLGDCKAPKVLGDIVESIAGAIFLDS-GRD 1742
+ + R ++D K K D VE+ GA+ +D G +
Sbjct: 187 QGNIATPTRVVKD----------------------KMSKRYADCVEAYIGALVIDRFGTE 224
Query: 1743 TSVVWQVFQPLLDP-------MVTPETLPMHPVRELQERCQQQAEG--LEYKASRSGNLA 1793
+ + + L + MV E L + EL E Q G L Y+
Sbjct: 225 FLDIKEWLEELSEKKLAKSSQMVIKEPLNKNAKNELAELLQINKLGHKLHYRKLTEMPPF 284
Query: 1794 TVEVYIDGVQVGVAQNPQKKMAQKLAA 1820
VEV I + + A+ + A+ AA
Sbjct: 285 RVEVKIGDILLDEAEGNSIREAEHRAA 311
>pdb|3RV1|A Chain A, Crystal Structure Of The N-Terminal And Rnase Iii Domains Of
K. Polysporus Dcr1 E224q Mutant
pdb|3RV1|B Chain B, Crystal Structure Of The N-Terminal And Rnase Iii Domains Of
K. Polysporus Dcr1 E224q Mutant
Length = 246
Score = 48.1 bits (113), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 40/66 (60%)
Query: 1403 ERAELLGDAYLKWVVSRFLFLKYPQKHEGQLTRMRQQMVSNLVLYQYALSKGLQSYIQAD 1462
ER E LGD++L +VS ++ ++P +EG L++M++ +V+N L+ ++ +Q +
Sbjct: 130 ERLEFLGDSWLGALVSYIVYTRFPSANEGMLSQMKESIVNNNNLFDWSTKLNFTKRLQGN 189
Query: 1463 RFAPSR 1468
P+R
Sbjct: 190 IATPTR 195
Score = 34.3 bits (77), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 28/115 (24%), Positives = 47/115 (40%), Gaps = 28/115 (24%)
Query: 1627 QRLEFVGDAVLDHLITKHLFFSYTNLPP---GRLTDLRAAAVNNENFARVAVKHKLHVHL 1683
+RLEF+GD+ L L++ + YT P G L+ ++ + VNN N + K L
Sbjct: 130 ERLEFLGDSWLGALVS---YIVYTRFPSANEGMLSQMKESIVNNNNLFDWSTKLNFTKRL 186
Query: 1684 RHGSSALDRQIRDFVKEVLEELLKPGFNSFGLGDCKAPKVLGDIVESIAGAIFLD 1738
+ + R ++D K K D V++ GA+ +D
Sbjct: 187 QGNIATPTRVVKD----------------------KMSKRYADCVQAYIGALVID 219
>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|B Chain B, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|C Chain C, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
pdb|2DB3|D Chain D, Structural Basis For Rna Unwinding By The Dead-Box Protein
Drosophila Vasa
Length = 434
Score = 46.6 bits (109), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 47/163 (28%), Positives = 75/163 (46%), Gaps = 30/163 (18%)
Query: 675 GELLDSHV-VSGGEHVDVIIGAAVADGKVT-------PKVQSLIKILLKYQHTEDFRAII 726
GE L ++V V+ G I+G A +D K T K LI+IL + I+
Sbjct: 255 GEFLKNYVFVAIG-----IVGGACSDVKQTIYEVNKYAKRSKLIEILSEQADG----TIV 305
Query: 727 FVERVVAALVLPKVFAE--LPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGRVTLL 784
FVE A L +E P+ S H + + Q ++ + F++G + +L
Sbjct: 306 FVETKRGADFLASFLSEKEFPTTSI--------HGDRLQS---QREQALRDFKNGSMKVL 354
Query: 785 VATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSD 827
+ATSVA GLDI+ VI +D+ + Y+ GR + G++
Sbjct: 355 IATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNN 397
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 45.1 bits (105), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 34/62 (54%)
Query: 764 MRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARK 823
M+ + + +FR G+V LV + + G+DI+ NVVI FD KT Y+ GR+ +
Sbjct: 292 MKQQERNKVFHEFRQGKVRTLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGR 351
Query: 824 PG 825
G
Sbjct: 352 FG 353
>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 = 44.7 bits (104), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 39/121 (32%), Positives = 56/121 (46%), Gaps = 16/121 (13%)
Query: 761 SQEMRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLA---------KTV 811
S EM Q I +FR+G+ +LV T+V G+D+ Q +VVI FDL +T
Sbjct: 297 SGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETY 356
Query: 812 LAYIQSRGRARKPGSDYILMIERGNLSHATFLRNARNSEETLRKEAIERTDLSHLKDTSR 871
L I GR K G L + + H+ + N R E +K IER D L + +
Sbjct: 357 LHRIGRTGRFGKRG----LAVNMVDSKHSMNILN-RIQEHFNKK--IERLDTDDLDEIEK 409
Query: 872 L 872
+
Sbjct: 410 I 410
>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 = 44.3 bits (103), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 39/121 (32%), Positives = 56/121 (46%), Gaps = 16/121 (13%)
Query: 761 SQEMRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLA---------KTV 811
S EM Q I +FR+G+ +LV T+V G+D+ Q +VVI FDL +T
Sbjct: 364 SGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETY 423
Query: 812 LAYIQSRGRARKPGSDYILMIERGNLSHATFLRNARNSEETLRKEAIERTDLSHLKDTSR 871
L I GR K G L + + H+ + N R E +K IER D L + +
Sbjct: 424 LHRIGRTGRFGKRG----LAVNMVDSKHSMNILN-RIQEHFNKK--IERLDTDDLDEIEK 476
Query: 872 L 872
+
Sbjct: 477 I 477
>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
Length = 170
Score = 44.3 bits (103), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 34/63 (53%)
Query: 763 EMRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRAR 822
EM + E I + +GRV +LVAT VA G+DI + V FD+ ++ Y+ GR
Sbjct: 63 EMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTA 122
Query: 823 KPG 825
+ G
Sbjct: 123 RAG 125
>pdb|2FFL|A Chain A, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2FFL|B Chain B, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2FFL|C Chain C, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2FFL|D Chain D, Crystal Structure Of Dicer From Giardia Intestinalis
pdb|2QVW|A Chain A, Structure Of Giardia Dicer Refined Against Twinned Data
pdb|2QVW|B Chain B, Structure Of Giardia Dicer Refined Against Twinned Data
pdb|2QVW|C Chain C, Structure Of Giardia Dicer Refined Against Twinned Data
pdb|2QVW|D Chain D, Structure Of Giardia Dicer Refined Against Twinned Data
Length = 756
Score = 43.9 bits (102), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/45 (48%), Positives = 29/45 (64%)
Query: 1402 YERAELLGDAYLKWVVSRFLFLKYPQKHEGQLTRMRQQMVSNLVL 1446
Y++ ELLGDA+LK ++ L +P EG LTRMRQ +N VL
Sbjct: 647 YQKLELLGDAFLKCSLALHLHALHPTLTEGALTRMRQSAETNSVL 691
Score = 37.4 bits (85), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 34/122 (27%), Positives = 48/122 (39%), Gaps = 31/122 (25%)
Query: 1626 YQRLEFVGDAVLDHLITKHLFFSYTNLPPGRLTDLRAAAVNNENFARVAVKHKLHVHLRH 1685
YQ+LE +GDA L + HL + L G LT +R +A N R
Sbjct: 647 YQKLELLGDAFLKCSLALHLHALHPTLTEGALTRMRQSAETNSVLGR------------- 693
Query: 1686 GSSALDRQIRDFVKEVLEEL---LKPGFNSFGLGDCKAPKVLGDIVESIAGAIFLDSGRD 1742
L ++ V EV+ E ++P KV GD E+I AI L G +
Sbjct: 694 ----LTKRFPSVVSEVIIESHPKIQPD-----------SKVYGDTFEAILAAILLACGEE 738
Query: 1743 TS 1744
+
Sbjct: 739 AA 740
Score = 37.0 bits (84), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 29/54 (53%)
Query: 1402 YERAELLGDAYLKWVVSRFLFLKYPQKHEGQLTRMRQQMVSNLVLYQYALSKGL 1455
++R ELLGDA L ++V+ L +P G L ++ ++V N L + GL
Sbjct: 334 FQRLELLGDAVLGFIVTARLLCLFPDASVGTLVELKMELVRNEALNYLVQTLGL 387
Score = 36.2 bits (82), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 25/43 (58%)
Query: 1626 YQRLEFVGDAVLDHLITKHLFFSYTNLPPGRLTDLRAAAVNNE 1668
+QRLE +GDAVL ++T L + + G L +L+ V NE
Sbjct: 334 FQRLELLGDAVLGFIVTARLLCLFPDASVGTLVELKMELVRNE 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 = 43.5 bits (101), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 29/47 (61%)
Query: 761 SQEMRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDL 807
S EM Q I +FR+G+ +LV T+V G+D+ Q +VVI FDL
Sbjct: 334 SGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDL 380
>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An
Atp-analogue And Rna
Length = 424
Score = 43.5 bits (101), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 29/47 (61%)
Query: 761 SQEMRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDL 807
S EM Q I +FR+G+ +LV T+V G+D+ Q +VVI FDL
Sbjct: 313 SGEMMVEQRAAVIERFREGKEKVLVTTNVCARGIDVEQVSVVINFDL 359
>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 = 43.5 bits (101), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 10/98 (10%)
Query: 761 SQEMRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLA---------KTV 811
S E+ Q I +FRDG+ +L+ T+V G+D++Q +V+ FDL +T
Sbjct: 65 SGELTVEQRASIIQRFRDGKEKVLITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETY 124
Query: 812 LAYIQSRGRARKPGSDYILMIERGNLSHATFLRNARNS 849
L I GR K G + MIE L +++ NS
Sbjct: 125 LHRIGRTGRFGKKGLAF-NMIEVDELPSLMKIQDHFNS 161
>pdb|2FWR|A Chain A, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|B Chain B, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|C Chain C, Structure Of Archaeoglobus Fulgidis Xpb
pdb|2FWR|D Chain D, Structure Of Archaeoglobus Fulgidis Xpb
Length = 472
Score = 42.7 bits (99), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 35/120 (29%), Positives = 59/120 (49%), Gaps = 17/120 (14%)
Query: 705 KVQSLIKILLKYQHTEDFRAIIFVERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEM 764
K++ L +IL + H +D + IIF + KVF +P+++ H S+E
Sbjct: 336 KIRKLREILER--HRKD-KIIIFTRHNELVYRISKVFL-IPAIT---------HRTSREE 382
Query: 765 RTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKP 824
R +E + FR GR +V++ V +EG+D+ NV + + + YIQ GR +P
Sbjct: 383 R----EEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRP 438
>pdb|2FZL|A Chain A, Structure Of C-Terminal Domain Of Archaeoglobus Fulgidus
Xpb
Length = 219
Score = 42.7 bits (99), Expect = 0.002, Method: Composition-based stats.
Identities = 35/120 (29%), Positives = 59/120 (49%), Gaps = 17/120 (14%)
Query: 705 KVQSLIKILLKYQHTEDFRAIIFVERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEM 764
K++ L +IL + H +D + IIF + KVF +P+++ H S+E
Sbjct: 101 KIRKLREILER--HRKD-KIIIFTRHNELVYRISKVFL-IPAIT---------HRTSREE 147
Query: 765 RTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKP 824
R +E + FR GR +V++ V +EG+D+ NV + + + YIQ GR +P
Sbjct: 148 R----EEILEGFRTGRFRAIVSSQVLDEGIDVPDANVGVIMSGSGSAREYIQRLGRILRP 203
>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 = 42.0 bits (97), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 30/63 (47%)
Query: 763 EMRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRAR 822
+MR FR+G LV T + G+DI+ NVVI FD K Y+ GR+
Sbjct: 77 KMRQEHRNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSG 136
Query: 823 KPG 825
+ G
Sbjct: 137 RFG 139
>pdb|2VA8|A Chain A, Dna Repair Helicase Hel308
pdb|2VA8|B Chain B, Dna Repair Helicase Hel308
Length = 715
Score = 42.0 bits (97), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 41/154 (26%), Positives = 73/154 (47%), Gaps = 18/154 (11%)
Query: 326 TGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLVPKVPLVYQQAEVIR--EQTGYVVGHYC 383
TG+GKTLIA + I S L+ K A+++ P L ++ + E G+ V
Sbjct: 55 TGSGKTLIAEMGIISFL--LKNGGK---AIYVTPLRALTNEKYLTFKDWELIGFKVAMTS 109
Query: 384 GEMGQDFWDAQRWQREFDTKQVLVMTAQILLNILRHSIIKMEAINLLILDECHHAVKKHP 443
G+ D DA W + +D +++ T + L ++ RH + +N +LDE H+
Sbjct: 110 GDYDTD--DA--WLKNYD---IIITTYEKLDSLWRHRPEWLNEVNYFVLDELHYLNDPER 162
Query: 444 YSLVMSEFYHTTSKEKRPSVFGMTASPVNLKGVS 477
+V S T + KR ++ ++A+ N K ++
Sbjct: 163 GPVVES----VTIRAKRRNLLALSATISNYKQIA 192
>pdb|2P6N|A Chain A, Human Dead-box Rna Helicase Ddx41, Helicase Domain
pdb|2P6N|B Chain B, Human Dead-box Rna Helicase Ddx41, Helicase Domain
Length = 191
Score = 41.6 bits (96), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 753 ASLIGHNNSQEMRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVL 812
A I QE RT + I FR+G+ +LVAT VA +GLD VI +D+ + +
Sbjct: 81 AVAIHGGKDQEERT----KAIEAFREGKKDVLVATDVASKGLDFPAIQHVINYDMPEEIE 136
Query: 813 AYIQSRGRARKPGSDYI 829
Y+ GR G+ I
Sbjct: 137 NYVHRIGRTGCSGNTGI 153
>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56
Length = 391
Score = 40.0 bits (92), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 34/151 (22%), Positives = 70/151 (46%), Gaps = 13/151 (8%)
Query: 723 RAIIFVERVVAALVLPKVFAE--LPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGR 780
+ +IFV+ V + L ++ E P+++ I QE R + Q+ F+D +
Sbjct: 252 QVVIFVKSVQRCIALAQLLVEQNFPAIA-------IHRGMPQEERLSRYQQ----FKDFQ 300
Query: 781 VTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSDYILMIERGNLSHA 840
+LVAT++ G+DI + N+ +D+ + Y+ RA + G+ + + + + A
Sbjct: 301 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDA 360
Query: 841 TFLRNARNSEETLRKEAIERTDLSHLKDTSR 871
L + ++ E E + D+S + +R
Sbjct: 361 KILNDVQDRFEVNISELPDEIDISSYIEQTR 391
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 40.0 bits (92), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 34/151 (22%), Positives = 70/151 (46%), Gaps = 13/151 (8%)
Query: 723 RAIIFVERVVAALVLPKVFAE--LPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGR 780
+ +IFV+ V + L ++ E P+++ I QE R + Q+ F+D +
Sbjct: 251 QVVIFVKSVQRCIALAQLLVEQNFPAIA-------IHRGMPQEERLSRYQQ----FKDFQ 299
Query: 781 VTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSDYILMIERGNLSHA 840
+LVAT++ G+DI + N+ +D+ + Y+ RA + G+ + + + + A
Sbjct: 300 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDA 359
Query: 841 TFLRNARNSEETLRKEAIERTDLSHLKDTSR 871
L + ++ E E + D+S + +R
Sbjct: 360 KILNDVQDRFEVNISELPDEIDISSYIEQTR 390
>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 = 39.7 bits (91), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 27/47 (57%)
Query: 768 QMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAY 814
+ + + FR G V +LVAT VA GLDI Q ++V+ + L AY
Sbjct: 69 ERERVLGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRLPDRAEAY 115
>pdb|2HJV|A Chain A, Structure Of The Second Domain (Residues 207-368) Of The
Bacillus Subtilis Yxin Protein
pdb|2HJV|B Chain B, Structure Of The Second Domain (Residues 207-368) Of The
Bacillus Subtilis Yxin Protein
Length = 163
Score = 39.7 bits (91), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 31/56 (55%)
Query: 771 ETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGS 826
+ + +F+ G LVAT VA G+DI ++VI +DL +Y+ GR + G+
Sbjct: 76 DVMNEFKRGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGN 131
>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 = 39.3 bits (90), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 756 IGHNNSQ---EMRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVL 812
+GH +M + + + FR G V +LVAT VA GLDI Q ++V+ + +
Sbjct: 51 LGHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDVAARGLDIPQVDLVVHYRMPDRAE 110
Query: 813 AY 814
AY
Sbjct: 111 AY 112
>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp
Length = 386
Score = 39.3 bits (90), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 33/144 (22%), Positives = 67/144 (46%), Gaps = 13/144 (9%)
Query: 723 RAIIFVERVVAALVLPKVFAE--LPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGR 780
+ +IFV+ V + L ++ E P+++ I QE R + Q+ F+D +
Sbjct: 252 QVVIFVKSVQRCIALAQLLVEQNFPAIA-------IHRGMPQEERLSRYQQ----FKDFQ 300
Query: 781 VTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSDYILMIERGNLSHA 840
+LVAT++ G+DI + N+ +D+ + Y+ RA + G+ + + + + A
Sbjct: 301 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDA 360
Query: 841 TFLRNARNSEETLRKEAIERTDLS 864
L + ++ E E + D+S
Sbjct: 361 KILNDVQDRFEVNISELPDEIDIS 384
>pdb|1T5I|A Chain A, Crystal Structure Of The C-Terminal Domain Of Uap56
Length = 172
Score = 39.3 bits (90), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 34/151 (22%), Positives = 70/151 (46%), Gaps = 13/151 (8%)
Query: 723 RAIIFVERVVAALVLPKVFAE--LPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGR 780
+ +IFV+ V + L ++ E P+++ I QE R + Q+ F+D +
Sbjct: 33 QVVIFVKSVQRCIALAQLLVEQNFPAIA-------IHRGMPQEERLSRYQQ----FKDFQ 81
Query: 781 VTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSDYILMIERGNLSHA 840
+LVAT++ G+DI + N+ +D+ + Y+ RA + G+ + + + + A
Sbjct: 82 RRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDA 141
Query: 841 TFLRNARNSEETLRKEAIERTDLSHLKDTSR 871
L + ++ E E + D+S + +R
Sbjct: 142 KILNDVQDRFEVNISELPDEIDISSYIEQTR 172
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 39.3 bits (90), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 27/53 (50%)
Query: 773 IAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG 825
I FR+G +L+ T VA GLDI VI FD + + YI GR + G
Sbjct: 259 IDAFREGEYDMLITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMG 311
>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 = 38.5 bits (88), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 61/121 (50%), Gaps = 14/121 (11%)
Query: 318 KNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLVPKVPLVYQQAEVIR--EQT 375
KN + + T +GKTLIA + ++ + + Q K AV++VP L ++ + + E+
Sbjct: 40 KNALISIPTASGKTLIAEI---AMVHRILTQGGK--AVYIVPLKALAEEKFQEFQDWEKI 94
Query: 376 GYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLNILRHSIIKMEAINLLILDEC 435
G V G D+ W ++D +++ TA+ ++LRH ++ + +L+ DE
Sbjct: 95 GLRVAMATG----DYDSKDEWLGKYD---IIIATAEKFDSLLRHGSSWIKDVKILVADEI 147
Query: 436 H 436
H
Sbjct: 148 H 148
>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
pdb|1HV8|B Chain B, Crystal Structure Of A Dead Box Protein From The
Hyperthermophile Methanococcus Jannaschii
Length = 367
Score = 38.1 bits (87), Expect = 0.048, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 30/58 (51%)
Query: 768 QMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG 825
Q ++ I F+ ++ +L+AT V G+D+ N VI + L + +Y GR + G
Sbjct: 276 QREKVIRLFKQKKIRILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAG 333
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 38.1 bits (87), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 770 QETIAK-FRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG 825
+E+I K FR G +L++T V GLD+ Q +++I +DL YI GR+ + G
Sbjct: 279 RESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 335
>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|B Chain B, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|C Chain C, Crystal Structure Of Human Apo-Eif4aiii
pdb|2HXY|D Chain D, Crystal Structure Of Human Apo-Eif4aiii
Length = 391
Score = 37.7 bits (86), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 770 QETIAK-FRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG 825
+E+I K FR G +L++T V GLD+ Q +++I +DL YI GR+ + G
Sbjct: 294 RESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 350
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 37.7 bits (86), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 770 QETIAK-FRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG 825
+E+I K FR G +L++T V GLD+ Q +++I +DL YI GR+ + G
Sbjct: 279 RESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 335
>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|B Chain B, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0S|A Chain A, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 410
Score = 37.7 bits (86), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 770 QETIAK-FRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG 825
+E+I K FR G +L++T V GLD+ Q +++I +DL YI GR+ + G
Sbjct: 315 RESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 371
>pdb|2HYI|C Chain C, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|I Chain I, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|3EX7|C Chain C, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|H Chain H, The Crystal Structure Of Ejc In Its Transition State
Length = 413
Score = 37.7 bits (86), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 770 QETIAK-FRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG 825
+E+I K FR G +L++T V GLD+ Q +++I +DL YI GR+ + G
Sbjct: 316 RESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 372
>pdb|1DI2|A Chain A, Crystal Structure Of A Dsrna-Binding Domain Complexed With
Dsrna: Molecular Basis Of Double-Stranded Rna-Protein
Interactions
pdb|1DI2|B Chain B, Crystal Structure Of A Dsrna-Binding Domain Complexed With
Dsrna: Molecular Basis Of Double-Stranded Rna-Protein
Interactions
Length = 69
Score = 37.7 bits (86), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 1857 TLNDICLRRNWPMPLYRCVREGGPAHAKRFTYAVRVNT 1894
+L ++ +++ W +P Y +E GP H + FT RV T
Sbjct: 5 SLQELAVQKGWRLPEYTVAQESGPPHKREFTITCRVET 42
>pdb|2XB2|A Chain A, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|X Chain X, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 411
Score = 37.7 bits (86), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 770 QETIAK-FRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG 825
+E+I K FR G +L++T V GLD+ Q +++I +DL YI GR+ + G
Sbjct: 316 RESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYG 372
>pdb|3ADL|A Chain A, Structure Of Trbp2 And Its Molecule Implications For Mirna
Processing
Length = 88
Score = 37.7 bits (86), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 1858 LNDICLRRNWPMPLYRCVREGGPAHAKRFTYAVRV 1892
L ++ +++ W +P Y +E GPAH K FT RV
Sbjct: 21 LQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRV 55
>pdb|2CPN|A Chain A, Solution Structure Of The Second Dsrbd Of Tar Rna-Binding
Protein 2
Length = 89
Score = 37.4 bits (85), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 1858 LNDICLRRNWPMPLYRCVREGGPAHAKRFTYAVRV 1892
L ++ +++ W +P Y +E GPAH K FT RV
Sbjct: 22 LQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRV 56
>pdb|3UWX|B Chain B, Crystal Structure Of Uvra-Uvrb Complex
Length = 683
Score = 36.6 bits (83), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 53/108 (49%), Gaps = 7/108 (6%)
Query: 729 ERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGRVTLLVATS 788
ER + + K+ +L ++K A + E++T + E I R G+ +LV +
Sbjct: 471 ERTLVTTLTKKMAEDLTD--YLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 528
Query: 789 VAEEGLDIRQCNVVIRFD-----LAKTVLAYIQSRGRARKPGSDYILM 831
+ EGLDI + ++V D ++ + IQ+ GRA + + +++M
Sbjct: 529 LLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIM 576
>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p
Length = 226
Score = 36.2 bits (82), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 31/134 (23%), Positives = 61/134 (45%), Gaps = 8/134 (5%)
Query: 309 LDVLEQAKKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLVPKVPLVYQQA 368
L +L +N IA ++G GKT L + + N ++ A+ L P L Q
Sbjct: 53 LPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNP---EDASPQAICLAPSRELARQTL 109
Query: 369 EVIREQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLNILRHSIIKMEAIN 428
EV++E +G + Q + + QV+V T +L+++R +++++ I
Sbjct: 110 EVVQE-----MGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRKLMQLQKIK 164
Query: 429 LLILDECHHAVKKH 442
+ +LDE + + +
Sbjct: 165 IFVLDEADNMLDQQ 178
>pdb|2FDC|A Chain A, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
pdb|2FDC|B Chain B, Structural Basis Of Dna Damage Recognition And Processing
By Uvrb: Crystal Structure Of A UvrbDNA COMPLEX
Length = 658
Score = 36.2 bits (82), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 53/108 (49%), Gaps = 7/108 (6%)
Query: 729 ERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGRVTLLVATS 788
ER + + K+ +L ++K A + E++T + E I R G+ +LV +
Sbjct: 446 ERTLVTTLTKKMAEDLTD--YLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 789 VAEEGLDIRQCNVVIRFD-----LAKTVLAYIQSRGRARKPGSDYILM 831
+ EGLDI + ++V D ++ + IQ+ GRA + + +++M
Sbjct: 504 LLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIM 551
>pdb|1D9Z|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb In
Complex With Atp
Length = 657
Score = 36.2 bits (82), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 53/108 (49%), Gaps = 7/108 (6%)
Query: 729 ERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGRVTLLVATS 788
ER + + K+ +L ++K A + E++T + E I R G+ +LV +
Sbjct: 445 ERTLVTTLTKKMAEDLTD--YLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 502
Query: 789 VAEEGLDIRQCNVVIRFD-----LAKTVLAYIQSRGRARKPGSDYILM 831
+ EGLDI + ++V D ++ + IQ+ GRA + + +++M
Sbjct: 503 LLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIM 550
>pdb|1D9X|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb
Length = 658
Score = 36.2 bits (82), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 53/108 (49%), Gaps = 7/108 (6%)
Query: 729 ERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGRVTLLVATS 788
ER + + K+ +L ++K A + E++T + E I R G+ +LV +
Sbjct: 446 ERTLVTTLTKKMAEDLTD--YLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 789 VAEEGLDIRQCNVVIRFD-----LAKTVLAYIQSRGRARKPGSDYILM 831
+ EGLDI + ++V D ++ + IQ+ GRA + + +++M
Sbjct: 504 LLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIM 551
>pdb|1T5L|A Chain A, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
pdb|1T5L|B Chain B, Crystal Structure Of The Dna Repair Protein Uvrb Point
Mutant Y96a Revealing A Novel Fold For Domain 2
Length = 658
Score = 36.2 bits (82), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 53/108 (49%), Gaps = 7/108 (6%)
Query: 729 ERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGRVTLLVATS 788
ER + + K+ +L ++K A + E++T + E I R G+ +LV +
Sbjct: 446 ERTLVTTLTKKMAEDLTD--YLKEAGIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 789 VAEEGLDIRQCNVVIRFD-----LAKTVLAYIQSRGRARKPGSDYILM 831
+ EGLDI + ++V D ++ + IQ+ GRA + + +++M
Sbjct: 504 LLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNANGHVIM 551
>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 = 35.8 bits (81), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 33/142 (23%), Positives = 65/142 (45%), Gaps = 12/142 (8%)
Query: 301 EEQARPYQLDVLEQAKKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLVPK 360
+E+A P +L +N IA ++G GKT L + + N ++ A+ L P
Sbjct: 32 QERALP----LLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNP---EDASPQAICLAPS 84
Query: 361 VPLVYQQAEVIREQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLNILRHS 420
L Q EV++E +G + Q + + QV+V T +L+++R
Sbjct: 85 RELARQTLEVVQE-----MGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRK 139
Query: 421 IIKMEAINLLILDECHHAVKKH 442
+++++ I + +LDE + + +
Sbjct: 140 LMQLQKIKIFVLDEADNMLDQQ 161
Score = 35.0 bits (79), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 757 GHNNSQEMRTFQMQE---TIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDL 807
GH S Q QE I FR+GR +L+ T+V G+DI ++V+ +DL
Sbjct: 267 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDL 320
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 35.8 bits (81), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 33/142 (23%), Positives = 65/142 (45%), Gaps = 12/142 (8%)
Query: 301 EEQARPYQLDVLEQAKKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLVPK 360
+E+A P +L +N IA ++G GKT L + + N ++ A+ L P
Sbjct: 32 QERALP----LLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNP---EDASPQAICLAPS 84
Query: 361 VPLVYQQAEVIREQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLNILRHS 420
L Q EV++E +G + Q + + QV+V T +L+++R
Sbjct: 85 RELARQTLEVVQE-----MGKFTKITSQLIVPDSFEKNKQINAQVIVGTPGTVLDLMRRK 139
Query: 421 IIKMEAINLLILDECHHAVKKH 442
+++++ I + +LDE + + +
Sbjct: 140 LMQLQKIKIFVLDEADNMLDQQ 161
Score = 35.0 bits (79), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 757 GHNNSQEMRTFQMQE---TIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDL 807
GH S Q QE I FR+GR +L+ T+V G+DI ++V+ +DL
Sbjct: 267 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDL 320
>pdb|1FUK|A Chain A, Crystal Structure Of The Carboxy Terminal Domain Of Yeast
Eif4a
Length = 165
Score = 35.8 bits (81), Expect = 0.23, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 768 QMQETIAK-FRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQ 816
Q ++TI K FR G +L++T + G+D++Q ++VI +DL YI
Sbjct: 67 QERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYIH 116
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 35.4 bits (80), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 35/78 (44%), Gaps = 9/78 (11%)
Query: 757 GHNNSQEMRTFQMQE---TIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTV-- 811
GH S Q QE I FR+GR +L+ T+V G+DI ++V+ +DL
Sbjct: 59 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANG 118
Query: 812 ----LAYIQSRGRARKPG 825
YI GR + G
Sbjct: 119 QADPATYIHRIGRTGRFG 136
>pdb|1GM5|A Chain A, Structure Of Recg Bound To Three-Way Dna Junction
Length = 780
Score = 35.4 bits (80), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 9/61 (14%)
Query: 772 TIAKFRDGRVTLLVATSVAEEGLDIRQCNVVI-----RFDLAKTVLAYIQSRGRARKPGS 826
+ +F +GR +LV+T+V E G+D+ + NV++ RF LA+ Q RGR + G
Sbjct: 631 VMLEFAEGRYDILVSTTVIEVGIDVPRANVMVIENPERFGLAQLH----QLRGRVGRGGQ 686
Query: 827 D 827
+
Sbjct: 687 E 687
>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex
pdb|3V4R|B Chain B, Crystal Structure Of A Uvrb Dimer-Dna Complex
Length = 667
Score = 35.4 bits (80), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 52/108 (48%), Gaps = 7/108 (6%)
Query: 729 ERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGRVTLLVATS 788
ERV+ + K+ +L ++K + + E++T + E I R G+ +LV +
Sbjct: 452 ERVLVTTLTKKMSEDLTD--YLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 509
Query: 789 VAEEGLDIRQCNVVIRFD-----LAKTVLAYIQSRGRARKPGSDYILM 831
+ EGLDI + ++V D ++ + IQ+ GRA + ++M
Sbjct: 510 LLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIM 557
>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase
Activity Of Uvrb
pdb|2NMV|A Chain A, Damage Detection By The Uvrabc Pathway: Crystal Structure
Of Uvrb Bound To Fluorescein-Adducted Dna
Length = 661
Score = 35.4 bits (80), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 27/108 (25%), Positives = 52/108 (48%), Gaps = 7/108 (6%)
Query: 729 ERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGRVTLLVATS 788
ERV+ + K+ +L ++K + + E++T + E I R G+ +LV +
Sbjct: 446 ERVLVTTLTKKMSEDLTD--YLKEIGIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN 503
Query: 789 VAEEGLDIRQCNVVIRFD-----LAKTVLAYIQSRGRARKPGSDYILM 831
+ EGLDI + ++V D ++ + IQ+ GRA + ++M
Sbjct: 504 LLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNAEGRVIM 551
>pdb|2XFM|A Chain A, Complex Structure Of The Miwi Paz Domain Bound To Methylated
Single Stranded Rna
Length = 150
Score = 35.0 bits (79), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 1232 AGDLEGRIVTAAHSGKRFYVESIRYEMTAESSFPRKEGYLGPLEYSSYADYYKQKYGVEL 1291
+ +L G IV ++ K + V+ I ++ +S+F + +G S+ +YY+++Y E+
Sbjct: 26 SKELIGLIVLTKYNNKTYRVDDIDWDQNPKSTFKKADG-----SEVSFLEYYRKQYNQEI 80
Query: 1292 IFKKQPLI 1299
KQP++
Sbjct: 81 TDLKQPVL 88
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 35.0 bits (79), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 9/78 (11%)
Query: 757 GHNNSQEMRTFQMQE---TIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTV-- 811
GH S Q QE I FR+GR +L+ T+V G+DI + V+ +DL
Sbjct: 61 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANG 120
Query: 812 ----LAYIQSRGRARKPG 825
YI GR + G
Sbjct: 121 QADPATYIHRIGRTGRFG 138
>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a
pdb|1FUU|B Chain B, Yeast Initiation Factor 4a
Length = 394
Score = 35.0 bits (79), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 768 QMQETIAK-FRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYI 815
Q ++TI K FR G +L++T + G+D++Q ++VI +DL YI
Sbjct: 296 QERDTIXKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYI 344
>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 = 35.0 bits (79), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 9/78 (11%)
Query: 757 GHNNSQEMRTFQMQE---TIAKFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTV-- 811
GH S Q QE I FR+GR +L+ T+V G+DI + V+ +DL
Sbjct: 60 GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSXVVNYDLPTLANG 119
Query: 812 ----LAYIQSRGRARKPG 825
YI GR + G
Sbjct: 120 QADPATYIHRIGRTGRFG 137
>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 = 34.7 bits (78), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 768 QMQETIAK-FRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYI 815
Q ++TI K FR G +L++T + G+D++Q ++VI +DL YI
Sbjct: 297 QERDTIMKEFRSGSSRILISTDLLARGIDVQQVSLVINYDLPANKENYI 345
>pdb|2L5C|A Chain A, Solution Structures Of Human Piwi-Like 1 Paz Domain
pdb|2L5D|A Chain A, Solution Structures Of Human Piwi-Like 1 Paz Domain With
Ssrna (5'- Pugaca)
Length = 134
Score = 34.7 bits (78), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 1232 AGDLEGRIVTAAHSGKRFYVESIRYEMTAESSFPRKEGYLGPLEYSSYADYYKQKYGVEL 1291
+ +L G +V ++ K + V+ I ++ +S+F + +G S+ +YY+++Y E+
Sbjct: 35 SKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADG-----SEVSFLEYYRKQYNQEI 89
Query: 1292 IFKKQPLI 1299
KQP++
Sbjct: 90 TDLKQPVL 97
>pdb|2WV9|A Chain A, Crystal Structure Of The Ns3 Protease-Helicase From Murray
Valley Encephalitis Virus
Length = 673
Score = 34.3 bits (77), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 40/174 (22%), Positives = 73/174 (41%), Gaps = 23/174 (13%)
Query: 297 EKMPEEQARPYQLDVLEQAKKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVF 356
E++ E Y ++L+ K++ T+ L GAGKT +L + I + +Q K++
Sbjct: 223 ERVEEPVPEAYNPEMLK--KRQLTVLDLHPGAGKT--RRILPQIIKDAIQ---KRLRTAV 275
Query: 357 LVPKVPLVYQQAEVIREQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLNI 416
L P + + AE +R G V + + QRE +++ + L
Sbjct: 276 LAPTRVVAAEMAEALR---GLPVRYLTPAV----------QREHSGNEIVDVMCHATLTH 322
Query: 417 LRHSIIKMEAINLLILDECHHAVKKHPYSLVMSEFYHTTSKEKRPSVFGMTASP 470
S +++ NL ++DE H P S+ + T + + MTA+P
Sbjct: 323 RLMSPLRVPNYNLFVMDEAHFT---DPASIAARGYIATRVEAGEAAAIFMTATP 373
>pdb|3O3I|X Chain X, Crystal Structure Of Human Hiwi1 Paz Domain (Residues
277-399) In Complex With 14-Mer Rna (12-Bp + 2-Nt
Overhang) Containing 2'-Oh At Its 3'-End
Length = 124
Score = 33.9 bits (76), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 1232 AGDLEGRIVTAAHSGKRFYVESIRYEMTAESSFPRKEGYLGPLEYSSYADYYKQKYGVEL 1291
+ +L G +V ++ K + V+ I ++ +S+F + +G S+ +YY+++Y E+
Sbjct: 25 SKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADG-----SEVSFLEYYRKQYNQEI 79
Query: 1292 IFKKQPLI 1299
KQP++
Sbjct: 80 TDLKQPVL 87
>pdb|3O6E|X Chain X, Crystal Structure Of Human Hiwi1 Paz Domain (Residues
277-399) In Complex With 14-Mer Rna (12-Bp + 2-Nt
Overhang) Containing 2'-Och3 At Its 3'-End
Length = 124
Score = 33.9 bits (76), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 1232 AGDLEGRIVTAAHSGKRFYVESIRYEMTAESSFPRKEGYLGPLEYSSYADYYKQKYGVEL 1291
+ +L G +V ++ K + V+ I ++ +S+F + +G S+ +YY+++Y E+
Sbjct: 25 SKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADG-----SEVSFLEYYRKQYNQEI 79
Query: 1292 IFKKQPLI 1299
KQP++
Sbjct: 80 TDLKQPVL 87
>pdb|3O7X|A Chain A, Crystal Structure Of Human Hili Paz Domain
pdb|3O7X|B Chain B, Crystal Structure Of Human Hili Paz Domain
pdb|3O7X|C Chain C, Crystal Structure Of Human Hili Paz Domain
pdb|3O7X|D Chain D, Crystal Structure Of Human Hili Paz Domain
Length = 140
Score = 33.9 bits (76), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 1227 DSCANAGDLEGRIVTAAHSGKRFYVESIRYEMTAESSFPRKEGYLGPLEYSSYADYYKQK 1286
D C L G IV ++ + + ++ + + T + SF +G + ++ +YY +
Sbjct: 22 DECTKL--LVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDG-----KEITFLEYYSKN 74
Query: 1287 YGVELIFKKQPLIRGR 1302
YG+ + + QPL+ R
Sbjct: 75 YGITVKEEDQPLLIHR 90
>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 = 33.9 bits (76), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 756 IGHNNSQEMRTFQMQETIAKFRDGRVTLLVATSVAEEGLDIRQCNVVI 803
IGH +MR +++ + F R +LV T++ E G+DI N +I
Sbjct: 843 IGHG---QMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTII 887
>pdb|3QIR|A Chain A, Crystal Structure Of Piwil2 Paz Domain
pdb|3QIR|B Chain B, Crystal Structure Of Piwil2 Paz Domain
pdb|3QIR|C Chain C, Crystal Structure Of Piwil2 Paz Domain
pdb|3QIR|D Chain D, Crystal Structure Of Piwil2 Paz Domain
Length = 148
Score = 33.5 bits (75), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 1227 DSCANAGDLEGRIVTAAHSGKRFYVESIRYEMTAESSFPRKEGYLGPLEYSSYADYYKQK 1286
D C L G IV ++ + + ++ + + T + SF +G + ++ +YY +
Sbjct: 22 DECTKL--LVGNIVITRYNNRTYRIDDVDWNKTPKDSFTMSDG-----KEITFLEYYSKN 74
Query: 1287 YGVELIFKKQPLIRGR 1302
YG+ + + QPL+ R
Sbjct: 75 YGITVKEEDQPLLIHR 90
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 33.5 bits (75), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 44/187 (23%), Positives = 72/187 (38%), Gaps = 32/187 (17%)
Query: 670 NEIEEGELLDSHVVSGGEHVDVIIGAAVADGKVTPKVQSLIKILLKYQHTEDFRAIIFVE 729
NE E E +D VV + + I A ++ IK + +++AIIF
Sbjct: 249 NEPEAHERIDQSVVISEKFANSIFAAV-------EHIKKQIK-----ERDSNYKAIIFAP 296
Query: 730 RVVAALVLPKVFA-----ELPSLSFVKSASLIGHNN-SQEMRTFQMQETIAKFRDGRVTL 783
V L + +LP L F H +Q RT + +F+ +
Sbjct: 297 TVKFTSFLCSILKNEFKKDLPILEF--------HGKITQNKRT----SLVKRFKKDESGI 344
Query: 784 LVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSD--YILMIERGNLSHAT 841
LV T V G+D + V++ + + YI GR + G + +L I + L
Sbjct: 345 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVR 404
Query: 842 FLRNARN 848
L +A+N
Sbjct: 405 ELEDAKN 411
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 33.1 bits (74), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 44/187 (23%), Positives = 72/187 (38%), Gaps = 32/187 (17%)
Query: 670 NEIEEGELLDSHVVSGGEHVDVIIGAAVADGKVTPKVQSLIKILLKYQHTEDFRAIIFVE 729
NE E E +D VV + + I A ++ IK + +++AIIF
Sbjct: 300 NEPEAHERIDQSVVISEKFANSIFAAV-------EHIKKQIK-----ERDSNYKAIIFAP 347
Query: 730 RVVAALVLPKVFA-----ELPSLSFVKSASLIGHNN-SQEMRTFQMQETIAKFRDGRVTL 783
V L + +LP L F H +Q RT + +F+ +
Sbjct: 348 TVKFTSFLCSILKNEFKKDLPILEF--------HGKITQNKRT----SLVKRFKKDESGI 395
Query: 784 LVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSD--YILMIERGNLSHAT 841
LV T V G+D + V++ + + YI GR + G + +L I + L
Sbjct: 396 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVR 455
Query: 842 FLRNARN 848
L +A+N
Sbjct: 456 ELEDAKN 462
>pdb|3FHO|A Chain A, Structure Of S. Pombe Dbp5
pdb|3FHO|B Chain B, Structure Of S. Pombe Dbp5
Length = 508
Score = 33.1 bits (74), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 776 FRDGRVTLLVATSVAEEGLDIRQCNVVIRFDL 807
FR G +LV T+V G+D+ Q N+V+ +D+
Sbjct: 403 FRVGTSKVLVTTNVIARGIDVSQVNLVVNYDM 434
>pdb|3IZR|H Chain H, Localization Of The Large Subunit Ribosomal Proteins Into A
5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 258
Score = 33.1 bits (74), Expect = 1.7, Method: Composition-based stats.
Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 11/102 (10%)
Query: 1295 KQPLIRGRGVSYCKNLLSPRFEHSXXXXXXXXXILDKTYYVFLPPELCFIHPLPGSLVRG 1354
K+P++ V Y N ++ E S +D V P LC +P +V+G
Sbjct: 123 KKPIV----VKYGLNHVTYLIEQSKAQLVVIAHDVDPIELVVWLPALCRKMEVPYCIVKG 178
Query: 1355 AQRLPSIMRRVESMLL---AIQLKDKINYPVPASKILEALTA 1393
RL SI+ + + +L ++ +DK+ + SKILEA+ A
Sbjct: 179 KARLGSIVHKKTASVLCLTTVKNEDKLEF----SKILEAIKA 216
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 33.1 bits (74), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 44/187 (23%), Positives = 72/187 (38%), Gaps = 32/187 (17%)
Query: 670 NEIEEGELLDSHVVSGGEHVDVIIGAAVADGKVTPKVQSLIKILLKYQHTEDFRAIIFVE 729
NE E E +D VV + + I A ++ IK + +++AIIF
Sbjct: 249 NEPEAHERIDQSVVISEKFANSIFAAV-------EHIKKQIK-----ERDSNYKAIIFAP 296
Query: 730 RVVAALVLPKVFA-----ELPSLSFVKSASLIGHNN-SQEMRTFQMQETIAKFRDGRVTL 783
V L + +LP L F H +Q RT + +F+ +
Sbjct: 297 TVKFTSFLCSILKNEFKKDLPILEF--------HGKITQNKRT----SLVKRFKKDESGI 344
Query: 784 LVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSD--YILMIERGNLSHAT 841
LV T V G+D + V++ + + YI GR + G + +L I + L
Sbjct: 345 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVR 404
Query: 842 FLRNARN 848
L +A+N
Sbjct: 405 ELEDAKN 411
>pdb|3O7V|X Chain X, Crystal Structure Of Human Hiwi1 (V361m) Paz Domain
(Residues 277-399) In Complex With 14-Mer Rna (12-Bp +
2-Nt Overhang) Containing 2'-Och3 At Its 3'-End
Length = 124
Score = 33.1 bits (74), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 1232 AGDLEGRIVTAAHSGKRFYVESIRYEMTAESSFPRKEGYLGPLEYSSYADYYKQKYGVEL 1291
+ +L G +V ++ K + V+ I ++ +S+F + +G S+ +YY+++Y E+
Sbjct: 25 SKELIGLVVLTKYNNKTYRVDDIDWDQNPKSTFKKADG-----SEVSFLEYYRKQYNQEI 79
Query: 1292 IFKKQPLI 1299
KQP +
Sbjct: 80 TDLKQPXL 87
>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 = 32.7 bits (73), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 37/184 (20%), Positives = 82/184 (44%), Gaps = 16/184 (8%)
Query: 302 EQARPYQLDVLEQA-KKKNTIAFLETGAGKTLIAVLLIRSICNDLQRQNKKMLAVFLVPK 360
E+ P Q + +E+ KN + + T AGKTL+A + + ++ K ++++VP
Sbjct: 24 EELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAM------VREAIKGGKSLYVVPL 77
Query: 361 VPLVYQQAEVIR--EQTGYVVGHYCGEMGQDFWDAQRWQREFDTKQVLVMTAQILLNILR 418
L ++ E + E+ G +G G D + ++V T++ +++R
Sbjct: 78 RALAGEKYESFKKWEKIGLRIGISTG-------DYESRDEHLGDCDIIVTTSEKADSLIR 130
Query: 419 HSIIKMEAINLLILDECHHAVKKHPYSLVMSEFYHTTSKEKRPSVFGMTASPVNLKGVSS 478
+ ++A++ L++DE H + + + K V G++A+ N+ ++
Sbjct: 131 NRASWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPNVTEIAE 190
Query: 479 QVDC 482
+D
Sbjct: 191 WLDA 194
>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a
pdb|3EIQ|D Chain D, Crystal Structure Of Pdcd4-eif4a
Length = 414
Score = 32.3 bits (72), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 775 KFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQ 816
+FR G +L+ T + G+D++Q ++VI +DL YI
Sbjct: 325 EFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYIH 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 = 32.0 bits (71), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 775 KFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYI 815
+FR G +L+ T + G+D++Q ++VI +DL YI
Sbjct: 299 EFRSGSSRVLITTDLLARGIDVQQVSLVINYDLPTNRENYI 339
>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 32.0 bits (71), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 55/136 (40%), Gaps = 20/136 (14%)
Query: 721 DFRAIIFVERVVAALVLPKVFA-----ELPSLSFVKSASLIGHNN-SQEMRTFQMQETIA 774
+++AIIF V L + +LP L F H +Q RT +
Sbjct: 33 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEF--------HGKITQNKRT----SLVK 80
Query: 775 KFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSD--YILMI 832
+F+ +LV T V G+D + V++ + + YI GR + G + +L I
Sbjct: 81 RFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140
Query: 833 ERGNLSHATFLRNARN 848
+ L L +A+N
Sbjct: 141 CKDELPFVRELEDAKN 156
>pdb|2Z3Q|B Chain B, Crystal Structure Of The Il-15IL-15ra Complex
pdb|2Z3Q|D Chain D, Crystal Structure Of The Il-15IL-15ra Complex
pdb|2Z3R|B Chain B, Crystal Structure Of The Il-15IL-15ra Complex
pdb|2Z3R|D Chain D, Crystal Structure Of The Il-15IL-15ra Complex
pdb|2Z3R|F Chain F, Crystal Structure Of The Il-15IL-15ra Complex
pdb|2Z3R|H Chain H, Crystal Structure Of The Il-15IL-15ra Complex
pdb|2Z3R|J Chain J, Crystal Structure Of The Il-15IL-15ra Complex
pdb|2Z3R|L Chain L, Crystal Structure Of The Il-15IL-15ra Complex
pdb|2Z3R|N Chain N, Crystal Structure Of The Il-15IL-15ra Complex
pdb|2Z3R|P Chain P, Crystal Structure Of The Il-15IL-15ra Complex
Length = 107
Score = 32.0 bits (71), Expect = 3.8, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 1842 NGKKRKNGTQTFTRQTLNDICLRRNWPMPLYRCVREGGPAHAK 1884
+G KRK GT + T LN +W P +C+R+ H +
Sbjct: 36 SGFKRKAGTSSLTECVLNKATNVAHWTTPSLKCIRDPALVHQR 78
>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
pdb|4DB4|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
Length = 256
Score = 31.6 bits (70), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 55/136 (40%), Gaps = 20/136 (14%)
Query: 721 DFRAIIFVERVVAALVLPKVFA-----ELPSLSFVKSASLIGHNN-SQEMRTFQMQETIA 774
+++AIIF V L + +LP L F H +Q RT +
Sbjct: 33 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEF--------HGKITQNKRT----SLVK 80
Query: 775 KFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSD--YILMI 832
+F+ +LV T V G+D + V++ + + YI GR + G + +L I
Sbjct: 81 RFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140
Query: 833 ERGNLSHATFLRNARN 848
+ L L +A+N
Sbjct: 141 CKDELPFVRELEDAKN 156
>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|D Chain D, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 31.6 bits (70), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 55/136 (40%), Gaps = 20/136 (14%)
Query: 721 DFRAIIFVERVVAALVLPKVFA-----ELPSLSFVKSASLIGHNN-SQEMRTFQMQETIA 774
+++AIIF V L + +LP L F H +Q RT +
Sbjct: 33 NYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEF--------HGKITQNKRT----SLVK 80
Query: 775 KFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPGSD--YILMI 832
+F+ +LV T V G+D + V++ + + YI GR + G + +L I
Sbjct: 81 RFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFI 140
Query: 833 ERGNLSHATFLRNARN 848
+ L L +A+N
Sbjct: 141 CKDELPFVRELEDAKN 156
>pdb|1D2M|A Chain A, Uvrb Protein Of Thermus Thermophilus Hb8; A Nucleotide
Excision Repair Enzyme
Length = 665
Score = 31.6 bits (70), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 40/144 (27%), Positives = 64/144 (44%), Gaps = 15/144 (10%)
Query: 729 ERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGRVTLLVATS 788
ER + ++ ++ EL SF+ + E+ F+ Q I R G LV +
Sbjct: 441 ERTLVTVLTVRMAEEL--TSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN 498
Query: 789 VAEEGLDIRQCNVVIRFD-----LAKTVLAYIQSRGR-ARKPGSDYILMIERGNLSHATF 842
+ EGLDI + ++V D ++ + IQ+ GR AR + L +R +S A
Sbjct: 499 LLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADR--VSEAM- 555
Query: 843 LRNARNSEETLRKEAI-ERTDLSH 865
R EET R+ A+ E +L H
Sbjct: 556 ---QRAIEETNRRRALQEAYNLEH 576
>pdb|1C4O|A Chain A, Crystal Structure Of The Dna Nucleotide Excision Repair
Enzyme Uvrb From Thermus Thermophilus
Length = 664
Score = 31.6 bits (70), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 40/144 (27%), Positives = 64/144 (44%), Gaps = 15/144 (10%)
Query: 729 ERVVAALVLPKVFAELPSLSFVKSASLIGHNNSQEMRTFQMQETIAKFRDGRVTLLVATS 788
ER + ++ ++ EL SF+ + E+ F+ Q I R G LV +
Sbjct: 440 ERTLVTVLTVRMAEEL--TSFLVEHGIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN 497
Query: 789 VAEEGLDIRQCNVVIRFD-----LAKTVLAYIQSRGR-ARKPGSDYILMIERGNLSHATF 842
+ EGLDI + ++V D ++ + IQ+ GR AR + L +R +S A
Sbjct: 498 LLREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADR--VSEAM- 554
Query: 843 LRNARNSEETLRKEAI-ERTDLSH 865
R EET R+ A+ E +L H
Sbjct: 555 ---QRAIEETNRRRALQEAYNLEH 575
>pdb|1EUZ|A Chain A, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
pdb|1EUZ|B Chain B, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
pdb|1EUZ|C Chain C, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
pdb|1EUZ|D Chain D, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
pdb|1EUZ|E Chain E, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
pdb|1EUZ|F Chain F, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
Length = 419
Score = 31.6 bits (70), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 35/84 (41%), Gaps = 3/84 (3%)
Query: 1150 PDVYLGTNERTLGGDRREYGFGKLRHGMAFGQKSHPTYGIRGAIAQFDVVKASGLVPDRE 1209
PDVY TN + +G EY R G AFG + I G++ + + RE
Sbjct: 144 PDVY--TNPKIMGWMMDEYETIMRRKGPAFGVITGKPLSIGGSLGRGTATAQGAIFTIRE 201
Query: 1210 AMQIHNADMPTGKLMMADSCANAG 1233
A + D+ GK + NAG
Sbjct: 202 AAKALGIDL-KGKKIAVQGYGNAG 224
>pdb|2KHX|A Chain A, Drosha Double-Stranded Rna Binding Motif
Length = 85
Score = 31.6 bits (70), Expect = 5.1, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 6/59 (10%)
Query: 1869 MPLYRCVREGGPAHAKRFTYAVRVNTTDKGWTDECVGEPMPSVKKAKDSAAVLLLELLN 1927
+PLY+ ++ GP+HA+ +T AV KG C PS+++A+ AA+ LE N
Sbjct: 23 IPLYKTLQTVGPSHARTYTVAVYF----KGERIGC--GKGPSIQQAEMGAAMDALEKYN 75
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 31.2 bits (69), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%)
Query: 775 KFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG 825
KF+ + ++VAT G++ V+ FD+ + + +Y Q GRA + G
Sbjct: 281 KFQRDDLQIVVATVAFGXGINKPNVRFVVHFDIPRNIESYYQETGRAGRDG 331
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 31.2 bits (69), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 22/94 (23%), Positives = 47/94 (50%), Gaps = 5/94 (5%)
Query: 775 KFRDGRVTLLVATSVAEEGLDIRQCNVVIRFDLAKTVLAYIQSRGRARKPG--SDYILMI 832
KF+ + ++VAT G++ V+ FD+ + + +Y Q GRA + G ++ +L
Sbjct: 281 KFQRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFY 340
Query: 833 ERGNLSHATFLRNARNSEETLRKEAIERTDLSHL 866
+ +++ +LR + + + IER L+ +
Sbjct: 341 DPADMA---WLRRCLEEKPQGQLQDIERHKLNAM 371
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 0.134 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 55,075,890
Number of Sequences: 62578
Number of extensions: 2268365
Number of successful extensions: 5200
Number of sequences better than 100.0: 116
Number of HSP's better than 100.0 without gapping: 84
Number of HSP's successfully gapped in prelim test: 32
Number of HSP's that attempted gapping in prelim test: 4987
Number of HSP's gapped (non-prelim): 200
length of query: 1931
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1818
effective length of database: 7,902,023
effective search space: 14365877814
effective search space used: 14365877814
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: 59 (27.3 bits)