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= 002135
(961 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 105/454 (23%), Positives = 170/454 (37%), Gaps = 99/454 (21%)
Query: 242 DNTKSALKSTGISKLYSHQAESIMAS-LAGKNVVVATMTSSGKSLCYNLPVLEALSHDL- 299
+ KS LK GI Y QAE++ + L GKN +++ T+SGK+L + A+ H +
Sbjct: 10 ERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEI----AMVHRIL 65
Query: 300 --SSSALYMFPTKXXXXXXXXXXXXMTKAFDASIDIGVYDGDTTQKDRMWLRDNARLLIT 357
A+Y+ P K K + + + GD KD WL ++ T
Sbjct: 66 TQGGKAVYIVPLKALAEEKFQEFQDWEK---IGLRVAMATGDYDSKDE-WLGKYDIIIAT 121
Query: 358 NPDMLHMSILPYHGQFSRILSNLRLIAFSLVTTEVYLIFLFIRFVVIDEAHAYKGAFGCH 417
L HG S + ++++ LV E++LI +GA
Sbjct: 122 AE---KFDSLLRHG--SSWIKDVKI----LVADEIHLI-----------GSRDRGA---- 157
Query: 418 TALILRRLCRLCSHVYGSDPSFVFSTATSANPREHCMELANLSTLELIQNDGSPCAQKLF 477
L + +H+ G + +AT NP ELA ELI +D
Sbjct: 158 ------TLEVILAHMLGK-AQIIGLSATIGNPE----ELAEWLNAELIVSD--------- 197
Query: 478 VLWNPTSCLRSVLNKSQTDMDDTRNAANKTSSPISEVSY----------LFAEMVQHGLR 527
W P R V + +D + ++ SS E+ Y +F M + R
Sbjct: 198 --WRPVKLRRGVFYQGFVTWED--GSIDRFSS-WEELVYDAIRKKKGALIFVNMRRKAER 252
Query: 528 CIAFCRSRKLCELVLSYTREILEETAPHLVDS-------------ICVYRAGYVAEDRRR 574
+A S+K+ L+ L E A L ++ + + AG ++R
Sbjct: 253 -VALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVL 311
Query: 575 IERDFFGGKLCGVAATNALELGIDVGHIDVTLHLGFPGS--------IASLWQQAGRSGR 626
+E +F G + V AT L GI+ V + + S I + Q GR+GR
Sbjct: 312 VEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGR 371
Query: 627 RERPSLA---VYVAFEGP---LDQYFMKYPEKLF 654
+ + + + P ++ Y PEKLF
Sbjct: 372 PKYDEVGEGIIVSTSDDPREVMNHYIFGKPEKLF 405
>pdb|1OYY|A Chain A, Structure Of The Recq Catalytic Core Bound To Atp-Gamma-S
Length = 523
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 37/129 (28%), Positives = 56/129 (43%), Gaps = 16/129 (12%)
Query: 523 QHGLRCIAFCRSRKLCELVLSYTREILEETAPHLVD---SICVYRAGYVAEDRRRIERDF 579
Q G I +C SR +E+TA L S Y AG R ++ F
Sbjct: 234 QRGKSGIIYCNSRAK-----------VEDTAARLQSKGISAAAYHAGLENNVRADVQEKF 282
Query: 580 FGGKLCGVAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERPSLAVYVAFE 639
L V AT A +GI+ ++ +H P +I S +Q+ GR+GR P+ A+ F
Sbjct: 283 QRDDLQIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAML--FY 340
Query: 640 GPLDQYFMK 648
P D +++
Sbjct: 341 DPADMAWLR 349
Score = 37.0 bits (84), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 240 LLDNTKSALKST-GISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVL 292
L K L+ T G + Q E I L+G++ +V T GKSLCY +P L
Sbjct: 9 LESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPAL 62
>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna
Helicase From Sulfolobus Tokodaii
Length = 337
Score = 43.9 bits (102), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 242 DNTKSALKSTGISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEALSHDLSS 301
+ + A++ G Q+++I L GKNVVV T SGK+ Y +P+LE L
Sbjct: 3 EKIEQAIREMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILE-----LGM 57
Query: 302 SALYMFPTK 310
+L + PT+
Sbjct: 58 KSLVVTPTR 66
>pdb|1OYW|A Chain A, Structure Of The Recq Catalytic Core
Length = 523
Score = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 42/159 (26%), Positives = 64/159 (40%), Gaps = 18/159 (11%)
Query: 493 SQTDMDDTRNAANKTSSPISEVSYLFAEMVQHGLRCIAFCRSRKLCELVLSYTREILEET 552
S D + R + P+ ++ E Q G I +C SR +E+T
Sbjct: 206 SSFDRPNIRYXLXEKFKPLDQLXRYVQE--QRGKSGIIYCNSRAK-----------VEDT 252
Query: 553 APHLVD---SICVYRAGYVAEDRRRIERDFFGGKLCGVAATNALELGIDVGHIDVTLHLG 609
A L S Y AG R ++ F L V AT A GI+ ++ +H
Sbjct: 253 AARLQSKGISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAFGXGINKPNVRFVVHFD 312
Query: 610 FPGSIASLWQQAGRSGRRERPSLAVYVAFEGPLDQYFMK 648
P +I S +Q+ GR+GR P+ A F P D +++
Sbjct: 313 IPRNIESYYQETGRAGRDGLPAEAXL--FYDPADXAWLR 349
Score = 37.4 bits (85), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 240 LLDNTKSALKST-GISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVL 292
L K L+ T G + Q E I L+G++ +V T GKSLCY +P L
Sbjct: 9 LESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVXPTGGGKSLCYQIPAL 62
>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 = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 52/111 (46%), Gaps = 7/111 (6%)
Query: 235 EIPDALLDNTKSALKSTGISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLP-VLE 293
E+ +++ LK GI +L+ QAE++ +GKN+++A T++GK+L + V E
Sbjct: 5 ELAESISSYAVGILKEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVRE 64
Query: 294 ALSHDLSSSALYMFPTKXXXXXXXXXXXXMTKAFDASIDIGVYDGDTTQKD 344
A+ +LY+ P + K + IG+ GD +D
Sbjct: 65 AIK---GGKSLYVVPLRALAGEKYESFKKWEK---IGLRIGISTGDYESRD 109
>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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 57/121 (47%), Gaps = 10/121 (8%)
Query: 521 MVQHGLRCIAFCRSRKLCELVLSYTREILEETAPHLVDSICVYRAGYVAEDRRRIERDFF 580
M ++ CI FCR++ E V T E+ + P D I G + EDR + +F
Sbjct: 31 MTENPDSCIIFCRTK---EHVNQLTDELDDLGYP--CDKI---HGGMIQEDRFDVMNEFK 82
Query: 581 GGKLCGVAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGR--RERPSLAVYVAF 638
G+ + AT+ GID+ +I + ++ P S + GR+GR + +++ AF
Sbjct: 83 RGEYRYLVATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFVTAF 142
Query: 639 E 639
E
Sbjct: 143 E 143
>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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/106 (28%), Positives = 43/106 (40%), Gaps = 8/106 (7%)
Query: 529 IAFCRSRKLCELVLSYTREILEETAPHLVDSICVYRAGYVAEDRRRIERDFFGGKLCGVA 588
I FC S + EL L + L S A E R R+ DF G +
Sbjct: 48 IIFCNSSQRVEL--------LAKKISQLGYSCFYIHAKMRQEHRNRVFHDFRNGLCRNLV 99
Query: 589 ATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERPSLAV 634
T+ GID+ ++V ++ FP + + GRSGR LA+
Sbjct: 100 CTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAI 145
>pdb|2V1X|A Chain A, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2V1X|B Chain B, Crystal Structure Of Human Recq-Like Dna Helicase
pdb|2WWY|A Chain A, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
pdb|2WWY|B Chain B, Structure Of Human Recq-Like Helicase In Complex With A
Dna Substrate
Length = 591
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 563 YRAGYVAEDRRRIERDFFGGKLCGVAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAG 622
Y A ED+ + R + ++ V AT A +GID + +H S+ + +Q++G
Sbjct: 297 YHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESG 356
Query: 623 RSGRRE-RPSLAVYVAF 638
R+GR + + +Y F
Sbjct: 357 RAGRDDMKADCILYYGF 373
Score = 38.9 bits (89), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%)
Query: 253 ISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVL 292
+ K Q E+I ++AGK V + T GKSLCY LP L
Sbjct: 42 LEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPAL 81
>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p
Length = 400
Score = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/109 (24%), Positives = 49/109 (44%), Gaps = 10/109 (9%)
Query: 527 RCIAFCRSRKLCELVLSYTREILEETAPHLVDSICVY-RAGYVAEDRRRIERDFFGGKLC 585
+ I FC S EL+ ++ C Y A ++R ++ +F GK+
Sbjct: 260 QAIIFCNSTNRVELLAKKITDL---------GYSCYYSHARMKQQERNKVFHEFRQGKVR 310
Query: 586 GVAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERPSLAV 634
+ ++ L GID+ ++V ++ FP + + + GRSGR LA+
Sbjct: 311 TLVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAI 359
Score = 35.8 bits (81), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 4/110 (3%)
Query: 252 GISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEALSHDLSS-SALYMFPTK 310
G K Q E+I ++ G++++ +GK+ + +P LE + L+ AL M PT+
Sbjct: 40 GFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPKLNKIQALIMVPTR 99
Query: 311 XXXXXXXXXXXXMTKAFDASIDIGVYDGDTTQKDRMW-LRDNARLLITNP 359
+ K I V G T +D + L + +L+ P
Sbjct: 100 ELALQTSQVVRTLGK--HCGISCMVTTGGTNLRDDILRLNETVHILVGTP 147
>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
pdb|1VEC|B Chain B, Crystal Structure Of The N-Terminal Domain Of RckP54, A
Human Dead-Box Protein
Length = 206
Score = 39.3 bits (90), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 46/103 (44%), Gaps = 5/103 (4%)
Query: 260 QAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEALSHDLSS---SALYMFPTKXXXXXX 316
Q ESI +L+G++++ +GKS Y +P+LE L DL A+ + PT+
Sbjct: 30 QEESIPIALSGRDILARAKNGTGKSGAYLIPLLERL--DLKKDNIQAMVIVPTRELALQV 87
Query: 317 XXXXXXMTKAFDASIDIGVYDGDTTQKDRMWLRDNARLLITNP 359
++K + + G + D M L D ++I P
Sbjct: 88 SQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATP 130
>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 = 39.3 bits (90), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 43/175 (24%), Positives = 76/175 (43%), Gaps = 14/175 (8%)
Query: 470 SPCAQKLFVLWNPTSCLRSVLNKSQTDMDDTRNAANKTSSPISEVSYLFAEMVQHGLRCI 529
+ C + +L + R +LN ++ D K ++ I E SY+ V R
Sbjct: 173 NACNKDKRILLFSATXPREILNLAKKYXGDYSFIKAKINANI-EQSYV---EVNENERFE 228
Query: 530 AFCR---SRKLCELVLSYTREILEETAPHLVDSICVYRAGYVAED-----RRRIERDFFG 581
A CR +++ LV T+ +E A L D ++AG + D R ++ R F
Sbjct: 229 ALCRLLKNKEFYGLVFCKTKRDTKELASXLRD--IGFKAGAIHGDLSQSQREKVIRLFKQ 286
Query: 582 GKLCGVAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERPSLAVYV 636
K+ + AT+ GIDV ++ ++ P + S + GR+GR + A+ +
Sbjct: 287 KKIRILIATDVXSRGIDVNDLNCVINYHLPQNPESYXHRIGRTGRAGKKGKAISI 341
Score = 35.4 bits (80), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 240 LLDNTKSALKSTGISKLYSHQAESIMASLAGK-NVVVATMTSSGKSLCYNLPVLEALSHD 298
L DN +A+++ G K Q + I L + N+V T SGK+ + +P++E ++ +
Sbjct: 13 LSDNILNAIRNKGFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNEN 72
Query: 299 LSSSALYMFPTK 310
A+ + PT+
Sbjct: 73 NGIEAIILTPTR 84
>pdb|3LY5|A Chain A, Ddx18 Dead-Domain
pdb|3LY5|B Chain B, Ddx18 Dead-Domain
Length = 262
Score = 38.9 bits (89), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 31/52 (59%)
Query: 242 DNTKSALKSTGISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVLE 293
+NT A+K G + + Q +SI L G++++ A T SGK+L + +P +E
Sbjct: 63 ENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVE 114
>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex
With Adp
Length = 236
Score = 38.1 bits (87), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 26/36 (72%)
Query: 260 QAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEAL 295
Q ++I +L GK+V+ A T SGK+L + +PVLEAL
Sbjct: 52 QKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEAL 87
>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 = 37.7 bits (86), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 80/399 (20%), Positives = 143/399 (35%), Gaps = 80/399 (20%)
Query: 238 DALLDN-TKSALK-STGISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEAL 295
D ++DN KS K T I K SI +G++++ T SGK+ + LP+L L
Sbjct: 65 DIIIDNVNKSGYKIPTPIQKC------SIPVISSGRDLMACAQTGSGKTAAFLLPILSKL 118
Query: 296 ---SHDLS---SSALYMFPTKXXXXXXXXXXXXMTKAFDASIDIG-VYDGDTTQKDRMWL 348
H+L + + PT+ AF++ + IG VY G + + +
Sbjct: 119 LEDPHELELGRPQVVIVSPTRELAIQIFNEARKF--AFESYLKIGIVYGGTSFRHQNECI 176
Query: 349 RDNARLLITNPDMLHMSILPYHGQFSRILSNLRLIAFSLVTTEVYLIFLFIRFVVIDEAH 408
++I P RL+ F ++ F RFVV+DEA
Sbjct: 177 TRGCHVVIATPG--------------------RLLDF---VDRTFITFEDTRFVVLDEAD 213
Query: 409 AYKGAFGCHTALILRRLCRLCSHVYGSDPSFVFSTATSANPREHCMELANLSTLELIQND 468
R+ + D + T + P + + E+ +
Sbjct: 214 ------------------RMLDMGFSEDMRRIM-THVTMRPEHQTLMFSATFPEEIQRMA 254
Query: 469 GSPCAQKLFVLWNPTSCLRSVLNKSQTDMDDTRNAANKTSSPISEVSYLFAEMVQHGLRC 528
G +FV ++ + +D+ T NK ++ S L + +
Sbjct: 255 GEFLKNYVFVAIG-------IVGGACSDVKQTIYEVNK----YAKRSKLIEILSEQADGT 303
Query: 529 IAFCRSRKLCELVLSYTREI-LEETAPHLVDSICVYRAGYVAEDRRRIERDFFGGKLCGV 587
I F +++ + + S+ E T+ H + R + RDF G + +
Sbjct: 304 IVFVETKRGADFLASFLSEKEFPTTSIH---------GDRLQSQREQALRDFKNGSMKVL 354
Query: 588 AATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGR 626
AT+ G+D+ +I ++ P I + GR+GR
Sbjct: 355 IATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGR 393
>pdb|1ZJ8|A Chain A, Structure Of Mycobacterium Tuberculosis Nira Protein
pdb|1ZJ8|B Chain B, Structure Of Mycobacterium Tuberculosis Nira Protein
pdb|1ZJ9|A Chain A, Structure Of Mycobacterium Tuberculosis Nira Protein
pdb|1ZJ9|B Chain B, Structure Of Mycobacterium Tuberculosis Nira Protein
Length = 566
Score = 33.9 bits (76), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 25/38 (65%)
Query: 229 RKAVLVEIPDALLDNTKSALKSTGISKLYSHQAESIMA 266
+K V+++IPDALLD+ + L + G+ SH ++MA
Sbjct: 390 QKLVILDIPDALLDDLIAGLDALGLQSRPSHWRRNLMA 427
>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1
pdb|2GXS|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXS|B Chain B, Hera N-Terminal Domain In Complex With Amp, Crystal Form 2
pdb|2GXU|A Chain A, Hera N-Terminal Domain In Complex With Orthophosphate,
Crystal Form 1
Length = 207
Score = 33.9 bits (76), Expect = 0.44, Method: Composition-based stats.
Identities = 30/129 (23%), Positives = 51/129 (39%), Gaps = 11/129 (8%)
Query: 247 ALKSTGISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEALS----HDLSSS 302
AL G++ QA ++ +L GK+++ T +GK+L + LP+ E L+
Sbjct: 15 ALHGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPR 74
Query: 303 ALYMFPTKXXXXXXXXXXXXMTKAFDASIDIGVYDGDTTQKDRMWLRDNARLLITNP--- 359
AL + PT+ + + VY G K + L A ++ P
Sbjct: 75 ALVLTPTRELALQVASELTAVAPHLKV---VAVYGGTGYGKQKEALLRGADAVVATPGRA 131
Query: 360 -DMLHMSIL 367
D L +L
Sbjct: 132 LDYLRQGVL 140
>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In
Complex With Amp
Length = 249
Score = 32.7 bits (73), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 252 GISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEALSHDLSSS-ALYMFPTK 310
G +K Q E+I +L G++++ T SGK+ + LP+L AL AL + PT+
Sbjct: 62 GWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETPQRLFALVLTPTR 121
>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWJ|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form
pdb|3MWK|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWK|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Complex
With 8-Oxo- Amp
pdb|3MWL|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3MWL|B Chain B, Q28e Mutant Of Hera N-Terminal Reca-Like Domain In Complex
With 8- Oxoadenosine
pdb|3NBF|A Chain A, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|B Chain B, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|C Chain C, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NBF|D Chain D, Q28e Mutant Of Hera Helicase N-Terminal Domain Bound To
8-Oxo-Adp
pdb|3NEJ|A Chain A, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
pdb|3NEJ|B Chain B, Q28e Mutant Of Hera Rna Helicase N-Terminal Domain -
Perfectly Twinned Hexagonal Form
Length = 207
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 29/129 (22%), Positives = 51/129 (39%), Gaps = 11/129 (8%)
Query: 247 ALKSTGISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEALS----HDLSSS 302
AL G++ +A ++ +L GK+++ T +GK+L + LP+ E L+
Sbjct: 15 ALHGRGLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQERGRKPR 74
Query: 303 ALYMFPTKXXXXXXXXXXXXMTKAFDASIDIGVYDGDTTQKDRMWLRDNARLLITNP--- 359
AL + PT+ + + VY G K + L A ++ P
Sbjct: 75 ALVLTPTRELALQVASELTAVAPHLKV---VAVYGGTGYGKQKEALLRGADAVVATPGRA 131
Query: 360 -DMLHMSIL 367
D L +L
Sbjct: 132 LDYLRQGVL 140
>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In
Complex With Adp
Length = 245
Score = 32.3 bits (72), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 260 QAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEALSHDLSSS--ALYMFPTK 310
Q ++I L G+ ++ + T SGK+L +++P+L L + AL + PT+
Sbjct: 56 QMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPANKGFRALIISPTR 108
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 6/81 (7%)
Query: 560 ICVYRAGYVAEDRRRIERDFFGGKLCGVAATNALELGIDVGHIDVTLHLGFP------GS 613
+ + ++R R+ DF G+ + TN L GID+ + + ++ P
Sbjct: 270 VSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQAD 329
Query: 614 IASLWQQAGRSGRRERPSLAV 634
A+ + GR+GR R +A+
Sbjct: 330 PATYIHRIGRTGRFGRKGVAI 350
>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3
pdb|3RRM|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Nup159, Gle1 H337r, Ip6
And Adp
pdb|3RRN|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Gle1 H337r And Ip6
Length = 395
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 6/81 (7%)
Query: 560 ICVYRAGYVAEDRRRIERDFFGGKLCGVAATNALELGIDVGHIDVTLHLGFP------GS 613
+ + ++R R+ DF G+ + TN L GID+ + + ++ P
Sbjct: 270 VSILHGDLQTQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQAD 329
Query: 614 IASLWQQAGRSGRRERPSLAV 634
A+ + GR+GR R +A+
Sbjct: 330 PATYIHRIGRTGRFGRKGVAI 350
>pdb|3DMI|A Chain A, Crystallization And Structural Analysis Of Cytochrome C6
From The Diatom Phaeodactylum Tricornutum At 1.5 A
Resolution
Length = 88
Score = 32.0 bits (71), Expect = 1.9, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 20/33 (60%)
Query: 37 RREKVILSHVKGALNQLEKFGVRVGIEDIENLA 69
R EK I+S V G N + FG R+ E+I N+A
Sbjct: 44 RTEKSIISQVTGGKNAMPAFGGRLSDEEIANVA 76
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 569 AEDRRRIERDFFGGKLCGVAATNALELGIDVGHIDVTLHLGFP------GSIASLWQQAG 622
++R R+ DF G+ + TN L GID+ + + ++ P A+ + G
Sbjct: 71 TQERDRLIDDFREGRSKVLITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIG 130
Query: 623 RSGRRERPSLAV 634
R+GR R +A+
Sbjct: 131 RTGRFGRKGVAI 142
>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 31.2 bits (69), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 24/108 (22%), Positives = 47/108 (43%), Gaps = 8/108 (7%)
Query: 527 RCIAFCRSRKLCELVLSYTREILEETAPHLVDSICVYRAGYVAEDRRRIERDFFGGKLCG 586
+ + FC +++ + + RE A V S+ ++R I ++F G
Sbjct: 242 QAVIFCNTKRKVDWLTEKMRE-----ANFTVSSM---HGDMPQKERESIMKEFRSGASRV 293
Query: 587 VAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERPSLAV 634
+ +T+ G+DV + + ++ P + + GRSGR R +AV
Sbjct: 294 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAV 341
>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0
A Resolution
Length = 374
Score = 31.2 bits (69), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 24/108 (22%), Positives = 47/108 (43%), Gaps = 8/108 (7%)
Query: 527 RCIAFCRSRKLCELVLSYTREILEETAPHLVDSICVYRAGYVAEDRRRIERDFFGGKLCG 586
+ + FC +++ + + RE A V S+ ++R I ++F G
Sbjct: 242 QAVIFCNTKRKVDWLTEKMRE-----ANFTVSSM---HGDMPQKERESIMKEFRSGASRV 293
Query: 587 VAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERPSLAV 634
+ +T+ G+DV + + ++ P + + GRSGR R +AV
Sbjct: 294 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAV 341
>pdb|4A4D|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Dead-Box Rna Helicase Ddx5 (P68)
Length = 253
Score = 30.8 bits (68), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 28/55 (50%)
Query: 243 NTKSALKSTGISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEALSH 297
N + ++ + QA+ +L+G ++V T SGK+L Y LP + ++H
Sbjct: 53 NVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINH 107
>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 = 30.8 bits (68), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 23/108 (21%), Positives = 47/108 (43%), Gaps = 8/108 (7%)
Query: 527 RCIAFCRSRKLCELVLSYTREILEETAPHLVDSICVYRAGYVAEDRRRIERDFFGGKLCG 586
+ + FC +++ + + RE A V S+ ++R I ++F G
Sbjct: 257 QAVIFCNTKRKVDWLTEKMRE-----ANFTVSSM---HGDMPQKERESIMKEFRSGASRV 308
Query: 587 VAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERPSLAV 634
+ +T+ G+DV + + ++ P + + GRSGR R +A+
Sbjct: 309 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI 356
>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 = 30.8 bits (68), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 23/108 (21%), Positives = 47/108 (43%), Gaps = 8/108 (7%)
Query: 527 RCIAFCRSRKLCELVLSYTREILEETAPHLVDSICVYRAGYVAEDRRRIERDFFGGKLCG 586
+ + FC +++ + + RE A V S+ ++R I ++F G
Sbjct: 279 QAVIFCNTKRKVDWLTEKMRE-----ANFTVSSM---HGDMPQKERESIMKEFRSGASRV 330
Query: 587 VAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERPSLAV 634
+ +T+ G+DV + + ++ P + + GRSGR R +A+
Sbjct: 331 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI 378
>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 = 30.8 bits (68), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 23/108 (21%), Positives = 47/108 (43%), Gaps = 8/108 (7%)
Query: 527 RCIAFCRSRKLCELVLSYTREILEETAPHLVDSICVYRAGYVAEDRRRIERDFFGGKLCG 586
+ + FC +++ + + RE A V S+ ++R I ++F G
Sbjct: 279 QAVIFCNTKRKVDWLTEKMRE-----ANFTVSSM---HGDMPQKERESIMKEFRSGASRV 330
Query: 587 VAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERPSLAV 634
+ +T+ G+DV + + ++ P + + GRSGR R +A+
Sbjct: 331 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI 378
>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 = 30.8 bits (68), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 23/108 (21%), Positives = 47/108 (43%), Gaps = 8/108 (7%)
Query: 527 RCIAFCRSRKLCELVLSYTREILEETAPHLVDSICVYRAGYVAEDRRRIERDFFGGKLCG 586
+ + FC +++ + + RE A V S+ ++R I ++F G
Sbjct: 278 QAVIFCNTKRKVDWLTEKMRE-----ANFTVSSM---HGDMPQKERESIMKEFRSGASRV 329
Query: 587 VAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERPSLAV 634
+ +T+ G+DV + + ++ P + + GRSGR R +A+
Sbjct: 330 LISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAI 377
>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I
In Complex With Adp
pdb|3FE2|B Chain B, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I
In Complex With Adp
Length = 242
Score = 30.8 bits (68), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 28/55 (50%)
Query: 243 NTKSALKSTGISKLYSHQAESIMASLAGKNVVVATMTSSGKSLCYNLPVLEALSH 297
N + ++ + QA+ +L+G ++V T SGK+L Y LP + ++H
Sbjct: 39 NVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINH 93
>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 = 30.4 bits (67), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 4/106 (3%)
Query: 571 DRRRIERDFFGGKLCGVAATNALELGIDVGHIDVTLHLGFPGSIASLWQQAGRSGRRERP 630
+++ + F GK+ + AT E G+D+ ++ + G + ++ Q GR+ E
Sbjct: 452 EQKEVISKFRTGKINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARADEST 511
Query: 631 SLAVYVAFEGPLDQYFMK-YPEKLFKSPIECCH---IDAQNHKVLE 672
+ V + G +++ + + EK+ I C + HK+LE
Sbjct: 512 YVLVAHSGSGVIERETVNDFREKMMYKAIHCVQNMKPEEYAHKILE 557
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
0.320 0.134 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,183,371
Number of Sequences: 62578
Number of extensions: 1025953
Number of successful extensions: 2262
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 34
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2218
Number of HSP's gapped (non-prelim): 56
length of query: 961
length of database: 14,973,337
effective HSP length: 108
effective length of query: 853
effective length of database: 8,214,913
effective search space: 7007320789
effective search space used: 7007320789
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)