RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7792
(138 letters)
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 157 bits (400), Expect = 3e-50
Identities = 61/83 (73%), Positives = 72/83 (86%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VATDVASKGLDF I+HVINYDMP+++ENYVHRIGRTG SG TG+ATTFINK+ DESVL
Sbjct: 108 LVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGCSGNTGIATTFINKACDESVL 167
Query: 61 LDLKHLLLEARQRIPPFLAELES 83
+DLK LLLEA+Q++PP L L
Sbjct: 168 MDLKALLLEAKQKVPPVLQVLHC 190
>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation,
nucleotide-binding, hydrolase, RNA-binding, ATP-binding,
DNA-binding, nuclear protein; 1.91A {Homo sapiens}
Length = 185
Score = 149 bits (379), Expect = 3e-47
Identities = 44/84 (52%), Positives = 61/84 (72%), Gaps = 1/84 (1%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VAT VA++GLD +KHVIN+D+P D+E YVHRIGRTGR G GLAT+F N+ + ++
Sbjct: 100 LVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNE-RNINIT 158
Query: 61 LDLKHLLLEARQRIPPFLAELESE 84
DL LL+EA+Q +P +L + E
Sbjct: 159 KDLLDLLVEAKQEVPSWLENMAYE 182
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 149 bits (380), Expect = 7e-45
Identities = 44/84 (52%), Positives = 61/84 (72%), Gaps = 1/84 (1%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VAT VA++GLD +KHVIN+D+P D+E YVHRIGRTGR G GLAT+F N+ + ++
Sbjct: 330 LVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNE-RNINIT 388
Query: 61 LDLKHLLLEARQRIPPFLAELESE 84
DL LL+EA+Q +P +L + E
Sbjct: 389 KDLLDLLVEAKQEVPSWLENMAYE 412
>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex,
ATPase, riken structural genomics/proteomics initiative,
RSGI; HET: ANP; 2.20A {Drosophila melanogaster}
Length = 434
Score = 146 bits (372), Expect = 2e-43
Identities = 41/78 (52%), Positives = 55/78 (70%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
++AT VAS+GLD + IKHVINYDMP +++YVHRIGRTGR G G AT+F + D ++
Sbjct: 354 LIATSVASRGLDIKNIKHVINYDMPSKIDDYVHRIGRTGRVGNNGRATSFFDPEKDRAIA 413
Query: 61 LDLKHLLLEARQRIPPFL 78
DL +L + Q +P FL
Sbjct: 414 ADLVKILEGSGQTVPDFL 431
>3eaq_A Heat resistant RNA dependent ATPase; DEAD box RNA helicase, dimer,
ATP-binding, helicase, hydrolase, nucleotide-binding;
2.30A {Thermus thermophilus} PDB: 3ear_A 3eas_A
Length = 212
Score = 103 bits (259), Expect = 9e-29
Identities = 24/52 (46%), Positives = 34/52 (65%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
+VATDVA++GLD ++ V++Y +PD E Y HR GRTGR+G+ G
Sbjct: 85 LVATDVAARGLDIPQVDLVVHYRLPDRAEAYQHRSGRTGRAGRGGRVVLLYG 136
>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase;
1.95A {Bacillus subtilis}
Length = 163
Score = 101 bits (255), Expect = 9e-29
Identities = 33/75 (44%), Positives = 47/75 (62%), Gaps = 4/75 (5%)
Query: 2 VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLL 61
VATDVA++G+D E I VINYD+P + E+YVHR GRTGR+G G A +F+ + ++ L
Sbjct: 90 VATDVAARGIDIENISLVINYDLPLEKESYVHRTGRTGRAGNKGKAISFV-TAFEKRFLA 148
Query: 62 DLKHLLLEARQRIPP 76
D++ I
Sbjct: 149 DIEEY---IGFEIQK 160
>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene
regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19
c.37.1.19 PDB: 1xtj_A* 1xtk_A
Length = 391
Score = 106 bits (268), Expect = 1e-28
Identities = 30/85 (35%), Positives = 48/85 (56%), Gaps = 3/85 (3%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VAT++ +G+D E + NYDMP+D + Y+HR+ R GR G GLA TF++ ND +L
Sbjct: 304 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 363
Query: 61 LDLKHLLLEARQRIPPFLAELESET 85
D++ I E++ +
Sbjct: 364 NDVQDRF---EVNISELPDEIDISS 385
>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein,
ATPase, RNA binding protein; 3.00A {Methanocaldococcus
jannaschii} SCOP: c.37.1.19 c.37.1.19
Length = 367
Score = 106 bits (267), Expect = 1e-28
Identities = 28/52 (53%), Positives = 40/52 (76%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
++ATDV S+G+D ++ VINY +P + E+Y+HRIGRTGR+GK G A + IN
Sbjct: 292 LIATDVMSRGIDVNDLNCVINYHLPQNPESYMHRIGRTGRAGKKGKAISIIN 343
>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity
A; hydrolase inhibitor-hydrolase complex, DEAD box RNA
helicase; 2.90A {Escherichia coli}
Length = 170
Score = 101 bits (255), Expect = 1e-28
Identities = 30/82 (36%), Positives = 49/82 (59%), Gaps = 5/82 (6%)
Query: 2 VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLL 61
VATDVA++G+D ++ HV N+DMP + Y+HRIGRT R+G+ G A + + ++D +L
Sbjct: 85 VATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVE-AHDHLLLG 143
Query: 62 DLKHLLLEARQRIPP-FLAELE 82
+ + + I + EL
Sbjct: 144 KVGRYI---EEPIKARVIDELR 162
>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase;
RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo
sapiens} SCOP: c.37.1.19
Length = 172
Score = 100 bits (252), Expect = 3e-28
Identities = 30/85 (35%), Positives = 48/85 (56%), Gaps = 3/85 (3%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VAT++ +G+D E + NYDMP+D + Y+HR+ R GR G GLA TF++ ND +L
Sbjct: 85 LVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKIL 144
Query: 61 LDLKHLLLEARQRIPPFLAELESET 85
D++ I E++ +
Sbjct: 145 NDVQDRF---EVNISELPDEIDISS 166
>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA
helicase, DEAD-BOX, ATP-binding, HE hydrolase,
mitochondrion; HET: ANP; 1.90A {Saccharomyces
cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A*
Length = 563
Score = 106 bits (266), Expect = 6e-28
Identities = 31/92 (33%), Positives = 52/92 (56%), Gaps = 3/92 (3%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+V TDV ++G+DF + V+ +P ++ NY+HRIGRT RSGK G + FI K + +
Sbjct: 396 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKD-ELPFV 454
Query: 61 LDLKHLL--LEARQRIPPFLAELESETEKFLD 90
+L+ + A+Q E++SE + +
Sbjct: 455 RELEDAKNIVIAKQEKYEPSEEIKSEVLEAVT 486
>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA
recognition motif, ATP-BIND helicase,
nucleotide-binding; 2.80A {Thermus thermophilus}
Length = 300
Score = 103 bits (258), Expect = 6e-28
Identities = 25/51 (49%), Positives = 33/51 (64%)
Query: 2 VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
VATDVA++GLD ++ V++Y MPD E Y HR GRTGR+G+ G
Sbjct: 83 VATDVAARGLDIPQVDLVVHYRMPDRAEAYQHRSGRTGRAGRGGRVVLLYG 133
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 104 bits (263), Expect = 1e-27
Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 13/91 (14%)
Query: 2 VATDVASKGLDFEEIKHVINYDMPD------DVENYVHRIGRTGRSGKTGLATTFINKSN 55
V T+V ++G+D ++ V+NYDMP D + Y+HRIGRTGR G+ G++ F++
Sbjct: 412 VTTNVIARGIDVSQVNLVVNYDMPLDQAGRPDPQTYLHRIGRTGRFGRVGVSINFVHDKK 471
Query: 56 DESVLLDLKHLLLEARQRI----PPFLAELE 82
+ ++ ++ I ELE
Sbjct: 472 SWEEMNAIQEYF---QRPITRVPTDDYEELE 499
>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA
dependent ATPase, RNA helicase; HET: ANP; 1.91A
{Saccharomyces cerevisiae S288C}
Length = 579
Score = 105 bits (263), Expect = 1e-27
Identities = 31/92 (33%), Positives = 53/92 (57%), Gaps = 3/92 (3%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+V TDV ++G+DF + V+ +P ++ NY+HRIGRT RSGK G + FI K + +
Sbjct: 345 LVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKD-ELPFV 403
Query: 61 LDLKHL--LLEARQRIPPFLAELESETEKFLD 90
+L+ ++ A+Q E++SE + +
Sbjct: 404 RELEDAKNIVIAKQEKYEPSEEIKSEVLEAVT 435
>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD;
ATP-binding, hydrolase, nucleotide-binding, RNA binding
protein, structural genomics; 1.90A {Sulfolobus
tokodaii}
Length = 337
Score = 102 bits (256), Expect = 3e-27
Identities = 31/66 (46%), Positives = 45/66 (68%), Gaps = 2/66 (3%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
++ TDVAS+GLD ++ VIN+D P D+ Y+HRIGRTGR G+ G A TFI N+ +
Sbjct: 270 LITTDVASRGLDIPLVEKVINFDAPQDLRTYIHRIGRTGRMGRKGEAITFI--LNEYWLE 327
Query: 61 LDLKHL 66
++K +
Sbjct: 328 KEVKKV 333
>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding,
RNA binding protein; 2.10A {Saccharomyces cerevisiae}
SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A
Length = 400
Score = 102 bits (256), Expect = 6e-27
Identities = 30/87 (34%), Positives = 45/87 (51%), Gaps = 1/87 (1%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+V +D+ ++G+D + + VIN+D P E Y+HRIGR+GR G GLA I ND L
Sbjct: 312 LVCSDLLTRGIDIQAVNVVINFDFPKTAETYLHRIGRSGRFGHLGLAINLI-NWNDRFNL 370
Query: 61 LDLKHLLLEARQRIPPFLAELESETEK 87
++ L IP + + E
Sbjct: 371 YKIEQELGTEIAAIPATIDKSLYVAEN 397
>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation,
rRNA processing, mRNA splicing, mRNA transport; HET:
ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB:
2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B
2zu6_A
Length = 410
Score = 100 bits (252), Expect = 3e-26
Identities = 29/75 (38%), Positives = 50/75 (66%), Gaps = 4/75 (5%)
Query: 2 VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLL 61
++TDV ++GLD ++ +INYD+P++ E Y+HRIGR+GR G+ G+A F+ K++D +L
Sbjct: 331 ISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFV-KNDDIRILR 389
Query: 62 DLKHLLLEARQRIPP 76
D++ +I
Sbjct: 390 DIEQYY---STQIDE 401
>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis,
cell cycle, nucleus, phosph RNA-binding, ATP-binding,
helicase, hydrolase; 3.50A {Homo sapiens}
Length = 414
Score = 100 bits (251), Expect = 4e-26
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 4/76 (5%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
++ TD+ ++G+D +++ VINYD+P + ENY+HRIGR GR G+ G+A + D+ L
Sbjct: 334 LITTDLLARGIDVQQVSLVINYDLPTNRENYIHRIGRGGRFGRKGVAINMV-TEEDKRTL 392
Query: 61 LDLKHLLLEARQRIPP 76
D++ I
Sbjct: 393 RDIETFY---NTSIEE 405
>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein,
translation; 2.50A {Saccharomyces cerevisiae} SCOP:
c.37.1.19 PDB: 2vso_A* 2vsx_A*
Length = 394
Score = 99 bits (250), Expect = 4e-26
Identities = 29/81 (35%), Positives = 52/81 (64%), Gaps = 1/81 (1%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+++TD+ ++G+D +++ VINYD+P + ENY+HRIGR GR G+ G+A F+ + D +
Sbjct: 313 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFV-TNEDVGAM 371
Query: 61 LDLKHLLLEARQRIPPFLAEL 81
+L+ + +P +A L
Sbjct: 372 RELEKFYSTQIEELPSDIATL 392
>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein,
translation; 1.75A {Saccharomyces cerevisiae} SCOP:
c.37.1.19
Length = 165
Score = 92.6 bits (231), Expect = 4e-25
Identities = 29/83 (34%), Positives = 53/83 (63%), Gaps = 1/83 (1%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+++TD+ ++G+D +++ VINYD+P + ENY+HRIGR GR G+ G+A F+ + D +
Sbjct: 84 LISTDLLARGIDVQQVSLVINYDLPANKENYIHRIGRGGRFGRKGVAINFV-TNEDVGAM 142
Query: 61 LDLKHLLLEARQRIPPFLAELES 83
+L+ + +P +A L +
Sbjct: 143 RELEKFYSTQIEELPSDIATLLN 165
>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase,
mRNA-export, nuclear pore, hydrolase-RNA complex; HET:
ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A*
3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A
3pev_A* 3peu_A*
Length = 395
Score = 96.5 bits (241), Expect = 8e-25
Identities = 29/93 (31%), Positives = 50/93 (53%), Gaps = 7/93 (7%)
Query: 2 VATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKSN 55
+ T+V ++G+D + V+NYD+P D Y+HRIGRTGR G+ G+A +F++ N
Sbjct: 298 ITTNVLARGIDIPTVSMVVNYDLPTLANGQADPATYIHRIGRTGRFGRKGVAISFVHDKN 357
Query: 56 DESVLLDL-KHLLLEARQRIPPFLAELESETEK 87
++L + K+ R+P + + K
Sbjct: 358 SFNILSAIQKYFGDIEMTRVPTDDWDEVEKIVK 390
>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA
dependent ATPase, mRNA export, nucleocytoplasmic
transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens}
PDB: 3ews_A* 3g0h_A* 3fhc_B
Length = 412
Score = 94.5 bits (236), Expect = 5e-24
Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 13/91 (14%)
Query: 2 VATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKSN 55
V T+V ++G+D E++ VIN+D+P D E Y+HRIGRTGR GK GLA ++ +
Sbjct: 321 VTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 380
Query: 56 DESVLLDLKHLLLEARQRI----PPFLAELE 82
++L ++ ++I L E+E
Sbjct: 381 SMNILNRIQEHF---NKKIERLDTDDLDEIE 408
>2rb4_A ATP-dependent RNA helicase DDX25; rossmann fold, structural
genomics, structural consortium, SGC, alternative
initiation, ATP-binding, devel protein; 2.80A {Homo
sapiens}
Length = 175
Score = 90.0 bits (224), Expect = 7e-24
Identities = 30/89 (33%), Positives = 50/89 (56%), Gaps = 8/89 (8%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKS 54
++ T+V ++G+D +++ V+N+D+P D E Y+HRIGRTGR GK GLA I
Sbjct: 88 LITTNVCARGIDVKQVTIVVNFDLPVKQGEEPDYETYLHRIGRTGRFGKKGLAFNMIEV- 146
Query: 55 NDESVLLDL-KHLLLEARQRIPPFLAELE 82
++ L+ + H +Q + E+E
Sbjct: 147 DELPSLMKIQDHFNSSIKQLNAEDMDEIE 175
>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore
complex, nucleocytoplasmic trans mRNA export, protein
interaction, beta-propeller; HET: ADP; 3.19A {Homo
sapiens}
Length = 479
Score = 93.9 bits (234), Expect = 1e-23
Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 13/91 (14%)
Query: 2 VATDVASKGLDFEEIKHVINYDMP------DDVENYVHRIGRTGRSGKTGLATTFINKSN 55
V T+V ++G+D E++ VIN+D+P D E Y+HRIGRTGR GK GLA ++ +
Sbjct: 388 VTTNVCARGIDVEQVSVVINFDLPVDKDGNPDNETYLHRIGRTGRFGKRGLAVNMVDSKH 447
Query: 56 DESVLLDLKHLLLEARQRI----PPFLAELE 82
++L ++ ++I L E+E
Sbjct: 448 SMNILNRIQEHF---NKKIERLDTDDLDEIE 475
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 75.1 bits (185), Expect = 5e-17
Identities = 23/99 (23%), Positives = 39/99 (39%), Gaps = 9/99 (9%)
Query: 1 MVATDV----ASKGLDF-EEIKHVINYDMP--DDVENYVHRIGRTGRSGKTGL--ATTFI 51
++ ++G+D E IK+VI + P DV Y+ GR+ R L + I
Sbjct: 301 LIGVQAYYGKLTRGVDLPERIKYVIFWGTPSGPDVYTYIQASGRSSRILNGVLVKGVSVI 360
Query: 52 NKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLD 90
+ ++E LLL A + I E ++
Sbjct: 361 FEEDEEIFESLKTRLLLIAEEEIIEEAEANWKELVHEVE 399
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA
repair, DNA recombina hydrolase; 2.90A {Pyrococcus
furiosus} SCOP: c.37.1.19 c.37.1.19
Length = 494
Score = 61.0 bits (147), Expect = 5e-12
Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 1/65 (1%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VAT V +GLD E+ V+ Y+ + R GRTGR G + K +
Sbjct: 423 LVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH-MPGRVIILMAKGTRDEAY 481
Query: 61 LDLKH 65
Sbjct: 482 YWSSR 486
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 44.2 bits (103), Expect = 3e-06
Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 1/85 (1%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRT-GRSGKTGLATTFINKSNDESV 59
++AT VA +G+D + VI Y+ +V + GR R K L T+ E +
Sbjct: 465 LIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQI 524
Query: 60 LLDLKHLLLEARQRIPPFLAELESE 84
+ + ++ ++ R+ + + E
Sbjct: 525 NMYKEKMMNDSILRLQTWDEAVFRE 549
>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.70A {Anas platyrhynchos}
Length = 936
Score = 43.0 bits (100), Expect = 8e-06
Identities = 16/93 (17%), Positives = 35/93 (37%), Gaps = 8/93 (8%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
++AT VA +G+D + V+ Y+ +V + GR GR+ +K+
Sbjct: 698 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENE 755
Query: 61 L------DLKHLLLEARQRIPPFLAELESETEK 87
++ + +E Q+ + +
Sbjct: 756 KCNRYKEEMMNKAVEKIQKWDEETFAKKIHNLQ 788
>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*
Length = 556
Score = 43.0 bits (100), Expect = 8e-06
Identities = 21/102 (20%), Positives = 40/102 (39%), Gaps = 13/102 (12%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
++AT VA +G+D + V+ Y+ +V + GR GR+ +K+
Sbjct: 457 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENE 514
Query: 61 LDLKHL------LLEARQRIPPFLAELESETEKFLDLGGDER 96
++ +E Q+ E+ +K +L ER
Sbjct: 515 KCNRYKEEMMNKAVEKIQKWDE-----ETFAKKIHNLQMKER 551
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 42.0 bits (98), Expect = 2e-05
Identities = 20/103 (19%), Positives = 43/103 (41%), Gaps = 6/103 (5%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG--KTGLATTFINKSNDES 58
++ +++ S+G +F+ H++ +D+P + + RIGR R G + +S
Sbjct: 560 LLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQS 619
Query: 59 VLLDLKHLLLEARQRI----PPFLAELESETEKFLDLGGDERG 97
VL+ H L+A + + ++ +L G
Sbjct: 620 VLVRWYHEGLDAFEHTCPTGRTIYDSVYNDLINYLASPDQTEG 662
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 42.2 bits (98), Expect = 2e-05
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDES 58
++AT VA +G+D E VI Y+ +V + GR GR+ + + ++
Sbjct: 456 LIATSVADEGIDIAECNLVILYEYVGNVIKMIQTRGR-GRA-RDSKCFLLTSSADVIE 511
>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.40A {Anas platyrhynchos}
Length = 797
Score = 41.5 bits (96), Expect = 3e-05
Identities = 21/102 (20%), Positives = 40/102 (39%), Gaps = 13/102 (12%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
++AT VA +G+D + V+ Y+ +V + GR GR+ +K+
Sbjct: 698 LIATSVADEGIDIVQCNLVVLYEYSGNVTKMIQVRGR-GRA-AGSKCILVTSKTEVVENE 755
Query: 61 LDLKHL------LLEARQRIPPFLAELESETEKFLDLGGDER 96
++ +E Q+ E+ +K +L ER
Sbjct: 756 KCNRYKEEMMNKAVEKIQKWDE-----ETFAKKIHNLQMKER 792
>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix,
helix-turn-helix, ATP binding, Zn(2+) binding,
hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43
c.37.1.19 c.37.1.19 PDB: 1oyy_A*
Length = 523
Score = 33.3 bits (77), Expect = 0.016
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 19 VINYDMPDDVENYVHRIGRTGRSG 42
V+++D+P ++E+Y GR GR G
Sbjct: 308 VVHFDIPRNIESYYQETGRAGRDG 331
>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA
compl protease/ntpase/helicase, hydrolase; 1.95A
{Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A*
1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A*
3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A
Length = 666
Score = 33.1 bits (75), Expect = 0.022
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 21/67 (31%)
Query: 2 VATDVASKGL--------DF-EEIKHVINYD-----------MPDDVENYVHRIGRTGRS 41
VATD G D + +++ +P D + R GRTGR
Sbjct: 444 VATDALMTGYTGDFDSVIDCNTCVTQTVDFSLDPTFTIETTTVPQDAVSRSQRRGRTGR- 502
Query: 42 GKTGLAT 48
G+ G+
Sbjct: 503 GRRGIYR 509
>2fna_A Conserved hypothetical protein; structural genomics, joint center
for structural genomics, J protein structure
initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus
solfataricus} SCOP: a.4.5.11 c.37.1.20
Length = 357
Score = 32.7 bits (74), Expect = 0.024
Identities = 15/51 (29%), Positives = 23/51 (45%)
Query: 40 RSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLD 90
R+GK+ + IN+ N + LDL+ FL EL+ E K +
Sbjct: 40 RTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVK 90
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 32.2 bits (73), Expect = 0.043
Identities = 14/84 (16%), Positives = 24/84 (28%), Gaps = 26/84 (30%)
Query: 1 MVATDVASK--GLDFEEIKHVINYDMPDDVENYVH--RIGRTGRSGKTGLATTFINKSND 56
+V+ A G+ P ++ YVH +G SG G++
Sbjct: 1017 LVSVVEAFIASGIT-----------DPYEMYKYVHVSEVGNCSGSGMGGVSA-------- 1057
Query: 57 ESVLLDLKHLLLEARQRIPPFLAE 80
L + + L E
Sbjct: 1058 ---LRGMFKDRFKDEPVQNDILQE 1078
>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch
repair, nucleotide-binding, DNA-binding, polymorphism,
nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens}
PDB: 2wwy_A*
Length = 591
Score = 30.3 bits (69), Expect = 0.20
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 19 VINYDMPDDVENYVHRIGRTGRSGK 43
VI++ M +ENY GR GR
Sbjct: 339 VIHHSMSKSMENYYQESGRAGRDDM 363
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 30.2 bits (67), Expect = 0.25
Identities = 17/87 (19%), Positives = 29/87 (33%), Gaps = 32/87 (36%)
Query: 32 VHRIGRTGRSGKTGLAT-------------------TFINKSNDESVLLDLKHLLL---- 68
+ G G SGKT +A N ++ E+VL L+ LL
Sbjct: 155 ID--GVLG-SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211
Query: 69 ------EARQRIPPFLAELESETEKFL 89
+ I + +++E + L
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLL 238
>1u6p_A GAG polyprotein; MLV, A-minor K-turn, stem loop, bulge, G-U
mismatch, G-A MIS U mismatch, A-C mismatch, zinc finger,
NC, viral protein-RN; HET: AP7; NMR {Moloney murine
leukemia virus} SCOP: g.40.1.1 PDB: 1wwd_A 1wwe_A 1wwf_A
1wwg_A
Length = 56
Score = 27.8 bits (61), Expect = 0.26
Identities = 9/16 (56%), Positives = 9/16 (56%)
Query: 98 CAYCGGLGHRITACPK 113
CAYC GH CPK
Sbjct: 26 CAYCKEKGHWAKDCPK 41
>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex,
PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus
musculus} PDB: 3trz_A* 3ts0_A*
Length = 148
Score = 29.2 bits (65), Expect = 0.30
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 90 DLGGDERGCAYCGGLGHRITACP 112
L + C +C + H + +CP
Sbjct: 114 KLPPQPKKCHFCQSINHMVASCP 136
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA, transcription-RNA
complex; NMR {Homo sapiens}
Length = 74
Score = 28.0 bits (62), Expect = 0.31
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 96 RGCAYCGGLGHRITACPK 113
+ C +C + H + +CP
Sbjct: 47 KKCHFCQSISHMVASCPL 64
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding,
exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Length = 124
Score = 28.6 bits (63), Expect = 0.41
Identities = 7/22 (31%), Positives = 8/22 (36%)
Query: 92 GGDERGCAYCGGLGHRITACPK 113
C CGG GH C +
Sbjct: 102 PFHTIYCYNCGGKGHFGDDCKE 123
Score = 25.9 bits (56), Expect = 3.5
Identities = 6/16 (37%), Positives = 6/16 (37%)
Query: 98 CAYCGGLGHRITACPK 113
C C GH CP
Sbjct: 7 CNNCSQRGHLKKDCPH 22
>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 63
Score = 27.2 bits (60), Expect = 0.45
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 96 RGCAYCGGLGHRITACPK 113
+ C +C + H + +CP
Sbjct: 30 KKCHFCQSISHMVASCPL 47
Score = 25.3 bits (55), Expect = 2.4
Identities = 8/22 (36%), Positives = 8/22 (36%)
Query: 92 GGDERGCAYCGGLGHRITACPK 113
G C CGGL H C
Sbjct: 4 GSSGDRCYNCGGLDHHAKECKL 25
>1a6b_B Momulv, zinc finger protein NCP10; nucleocapsid protein,
intercalation, nucleic acid, retrovirus, viral
protein/DNA complex; HET: DNA; NMR {Synthetic} SCOP:
g.40.1.1
Length = 40
Score = 26.7 bits (58), Expect = 0.58
Identities = 10/21 (47%), Positives = 10/21 (47%)
Query: 94 DERGCAYCGGLGHRITACPKL 114
D CAYC GH CPK
Sbjct: 9 DRDQCAYCKEKGHWAKDCPKK 29
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein,
metal binding protein; NMR {Synthetic}
Length = 39
Score = 26.4 bits (58), Expect = 0.63
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 95 ERGCAYCGGLGHRITACPK 113
+ GC CG HR CPK
Sbjct: 21 QEGCWNCGSKEHRFAQCPK 39
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA
complex; NMR {Rous sarcoma virus}
Length = 61
Score = 26.4 bits (58), Expect = 0.97
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 92 GGDERGCAYCGGLGHRITACPK 113
G C C G+GH C K
Sbjct: 27 GNSRERCQLCNGMGHNAKQCRK 48
>3nyb_B Protein AIR2; polya RNA polymerase, zinc knuckle protein, RNA
surveillance binds to TRF4P/AIR2P heterodimer; 2.70A
{Saccharomyces cerevisiae}
Length = 83
Score = 26.9 bits (59), Expect = 0.97
Identities = 5/17 (29%), Positives = 6/17 (35%)
Query: 98 CAYCGGLGHRITACPKL 114
C C H CP +
Sbjct: 8 CTLCKSKKHSKERCPSI 24
Score = 26.5 bits (58), Expect = 1.4
Identities = 10/37 (27%), Positives = 15/37 (40%)
Query: 77 FLAELESETEKFLDLGGDERGCAYCGGLGHRITACPK 113
++ ++E K L C CGG GH C +
Sbjct: 28 YILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE 64
>3sn6_R Lysozyme, beta-2 adrenergic receptor; seven transmembrane receptor,
nanobody, G protein-coupled RE GPCR, signal
transduction, G protein signaling; HET: P0G; 3.20A
{Enterobacteria phage T4} PDB: 3kj6_A 2r4s_A 2r4r_A
Length = 514
Score = 28.0 bits (62), Expect = 1.2
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 100 YCGGLGHRITACPKLEAVQTKAASSIGR 127
Y G+GH +T P L A +++ +IGR
Sbjct: 39 YTIGIGHLLTKSPSLNAAKSELDKAIGR 66
>2ec7_A GAG polyprotein (PR55GAG); nucleocapsid protein, HIV-2, RNA
recognition, zinc finger, viral protein; NMR {Human
immunodeficiency virus type 2} SCOP: g.40.1.1
Length = 49
Score = 25.7 bits (56), Expect = 1.5
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 95 ERGCAYCGGLGHRITACPKLEA 116
+GC CG GH + CP+ +A
Sbjct: 27 RQGCWKCGKTGHVMAKCPERQA 48
>3ebh_A PFA-M1, M1 family aminopeptidase; hydrolase, metal-binding,
metalloprotease, P hydrolase inhibitor; HET: BES; 1.65A
{Plasmodium falciparum} PDB: 3ebg_A* 3ebi_A* 3q43_A*
3q44_A* 3t8v_A*
Length = 889
Score = 27.5 bits (61), Expect = 1.7
Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 6/72 (8%)
Query: 3 ATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLD 62
A + K + F+E + YD+ V G GL F N S+L
Sbjct: 230 ALECLKKSMAFDEDYFGLEYDLSRLNLVAVSDFN-VGAMENKGL-NIF----NANSLLAS 283
Query: 63 LKHLLLEARQRI 74
K+ + + RI
Sbjct: 284 KKNSIDFSYARI 295
>3ikh_A Carbohydrate kinase; transferase,kinase,SAD,ribose,D-ribose
metabolic process,ATP ribokinase, PFKB
family,11206L1,PSI-II,nysgxrc; HET: ATP; 1.88A
{Klebsiella pneumoniae subsp} PDB: 3i3y_A*
Length = 299
Score = 27.1 bits (61), Expect = 2.0
Identities = 10/48 (20%), Positives = 12/48 (25%), Gaps = 7/48 (14%)
Query: 82 ESETEKFLDLGGD-------ERGCAYCGGLGHRITACPKLEAVQTKAA 122
ESE E G G + EA+ T A
Sbjct: 185 ESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGA 232
>2whx_A Serine protease/ntpase/helicase NS3; transcription, hydrolase,
ATP-binding, reticulum, nucleotidyltransferase,
multifunctional enzyme; HET: ADP; 2.20A {Dengue virus 4}
PDB: 2vbc_A 2wzq_A
Length = 618
Score = 26.4 bits (58), Expect = 3.3
Identities = 26/120 (21%), Positives = 38/120 (31%), Gaps = 26/120 (21%)
Query: 2 VATDVASKGL--------DF-EEIKHVINYDMPDDVENYV----------HRIGRTGRSG 42
V TD++ G D +K VI D P+ V R GR GR
Sbjct: 406 VTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGR-N 464
Query: 43 KTGLATTFINKSNDESVLLDLKH-----LLLEARQRIPPFLAEL-ESETEKFLDLGGDER 96
++ + D H +LL+ + L E EK + G+ R
Sbjct: 465 PAQEDDQYVFSGDPLKNDEDHAHWTEAKMLLDNIYTPEGIIPTLFGPEREKTQAIDGEFR 524
>3ic4_A Glutaredoxin (GRX-1); structural genomics, PSI, MCSG, protein
structure initiative, midwest center for structural
genomic oxidoreductase; 1.70A {Archaeoglobus fulgidus}
Length = 92
Score = 25.3 bits (56), Expect = 3.3
Identities = 8/45 (17%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 8 SKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
+G+DFE I I+ ++ + + ++ SG +
Sbjct: 34 REGVDFEVIW--IDKLEGEERKKVIEKVHS--ISGSYSVPVVVKG 74
>1cl4_A Protein (GAG polyprotein); nucleocapsid protein, RNA binding
protein, retrovirus, viral protein; NMR {Mason-pfizer
monkey virus} SCOP: g.40.1.1 PDB: 1dsv_A
Length = 60
Score = 24.5 bits (53), Expect = 4.1
Identities = 6/29 (20%), Positives = 8/29 (27%)
Query: 96 RGCAYCGGLGHRITACPKLEAVQTKAASS 124
C CG GH C + +
Sbjct: 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVP 30
>3pl5_A SMU_165, putative uncharacterized protein; fatty acid binding
protein, lipid binding protein; HET: PLM; 2.04A
{Streptococcus mutans}
Length = 320
Score = 26.1 bits (58), Expect = 4.2
Identities = 6/46 (13%), Positives = 17/46 (36%), Gaps = 10/46 (21%)
Query: 3 ATDVASKGLDFEEI--------KHVINYDMPDDVENYVH--RIGRT 38
A +G +E + + + D++ + + R+ +T
Sbjct: 169 AAQAREEGKSLKETKELILDVGPRLRTFFLVDNLYHLMRGGRLSKT 214
>3fdj_A DEGV family protein; GUT microbiome, structural genomics, PSI-2,
protein ST initiative, midwest center for structural
genomics, MCSG; HET: MSE P6G PG4; 1.80A {Eubacterium
eligens}
Length = 278
Score = 26.0 bits (58), Expect = 4.3
Identities = 7/46 (15%), Positives = 14/46 (30%), Gaps = 10/46 (21%)
Query: 3 ATDVASKGLDFEEI--------KHVINYDMPDDVENYVH--RIGRT 38
+ +G FEEI + + + N R+ +
Sbjct: 129 LQQMIEEGKKFEEIDGAIDAYMQKTRLFCSLKSLHNLAQNGRVSKV 174
>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 55
Score = 24.4 bits (53), Expect = 4.6
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 98 CAYCGGLGHRITACP 112
C CG GH I CP
Sbjct: 10 CFRCGKPGHYIKNCP 24
>1pzx_A Hypothetical protein APC36103; structural genomics, two domains
containing mixed alpha/beta structures, PSI; HET: PLM;
2.00A {Geobacillus stearothermophilus} SCOP: c.119.1.1
Length = 289
Score = 26.0 bits (58), Expect = 4.6
Identities = 7/46 (15%), Positives = 19/46 (41%), Gaps = 10/46 (21%)
Query: 3 ATDVASKGLDFEEI--------KHVINYDMPDDVENYVH--RIGRT 38
A ++A + + + +H+ + D+++ RI +T
Sbjct: 135 AVELAKQNTPYNLLCETIESYCRHMEHIFTVDNLDYLARGGRISKT 180
>1a1t_A Nucleocapsid protein; stem-loop RNA, viral protein/RNA complex; NMR
{Human immunodeficiency virus 1} SCOP: g.40.1.1 PDB:
1mfs_A 1f6u_A* 1aaf_A 2l4l_A 2exf_A 2jzw_A* 1bj6_A*
1esk_A 1q3y_A 1q3z_A 2e1x_A 2iwj_A
Length = 55
Score = 24.6 bits (53), Expect = 4.7
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 95 ERGCAYCGGLGHRITACPKLEA 116
++GC CG GH++ C + +A
Sbjct: 33 KKGCWKCGKEGHQMKDCTERQA 54
>3o2q_B RNA polymerase II subunit A C-terminal domain PHO SSU72; heat
repeat, scaffold, phosphatase, polymerase II CTD, CIS-P
hydrolase; HET: SEP; 2.40A {Homo sapiens} PDB: 3o2s_B
Length = 214
Score = 25.6 bits (56), Expect = 5.1
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVEN 30
V D+ S+ + + HV+N D+ D+ E
Sbjct: 138 QVVEDLNSREQETCQPVHVVNVDIQDNHEE 167
>3jr7_A Uncharacterized EGV family protein COG1307; structural genomics,
PSI2, MCSG, protein struct initiative; HET: PG6; 2.00A
{Ruminococcus gnavus}
Length = 298
Score = 25.7 bits (57), Expect = 5.2
Identities = 6/46 (13%), Positives = 15/46 (32%), Gaps = 10/46 (21%)
Query: 3 ATDVASKGLDFEEI--------KHVINYDMPDDVENYVH--RIGRT 38
G+ FEE+ + Y + ++++ R+
Sbjct: 150 VQQCEKAGMTFEEVVESVECYIEEQHTYFVLENLDTLRKNGRLTGI 195
>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding,
viral nucleoprotein, endoplasmic reticulum, helicase,
hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A*
2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A
2bhr_A
Length = 451
Score = 26.0 bits (57), Expect = 5.4
Identities = 16/58 (27%), Positives = 20/58 (34%), Gaps = 19/58 (32%)
Query: 2 VATDVASKGL--------DF-EEIKHVINYDMPDDVENYV----------HRIGRTGR 40
V TD++ G D +K VI D P+ V R GR GR
Sbjct: 239 VTTDISEMGANFRAGRVIDPRRCLKPVILTDGPERVILAGPIPVTPASAAQRRGRIGR 296
>2hhp_A Poly(A) polymerase; template-independent RNA polymerase,
transferase; HET: FLC; 1.80A {Saccharomyces cerevisiae}
SCOP: a.160.1.1 d.218.1.3 d.58.16.1 PDB: 1fa0_A* 3c66_A*
2o1p_A 2q66_A*
Length = 530
Score = 26.0 bits (56), Expect = 6.0
Identities = 6/14 (42%), Positives = 10/14 (71%)
Query: 15 EIKHVINYDMPDDV 28
++ V YD+PD+V
Sbjct: 508 ALRFVKGYDLPDEV 521
>1yqe_A Hypothetical UPF0204 protein AF0625; AF0625,sulfur SAD, structural
genomics, PSI, protein structure initiative; 1.83A
{Archaeoglobus fulgidus} SCOP: c.56.7.1
Length = 282
Score = 25.7 bits (56), Expect = 6.5
Identities = 6/37 (16%), Positives = 14/37 (37%)
Query: 51 INKSNDESVLLDLKHLLLEARQRIPPFLAELESETEK 87
+ S E +++D K + ++ + E K
Sbjct: 235 VKLSEAEYIIIDEKSVNSAVKKIVNEAAEVAGVEVLK 271
>1s3e_A Amine oxidase [flavin-containing] B; human monoamine oxidase,
inhibitor binding, rasagiline, enantioselectivity,
oxidoreductase; HET: FAD RHP; 1.60A {Homo sapiens} SCOP:
c.3.1.2 d.16.1.5 PDB: 1gos_A* 1oj9_A* 1ojb_A* 1ojc_A*
1ojd_A* 1s2q_A* 1s2y_A* 1oja_A* 1s3b_A* 2bk3_A* 2byb_A*
2c64_A* 2c65_A* 2c66_A* 2c67_A* 2c70_A* 2v5z_A* 2v60_A*
2v61_A* 2vrl_A* ...
Length = 520
Score = 25.6 bits (56), Expect = 7.1
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 66 LLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITA 110
++LEAR R+ + T + + + G +Y G +RI
Sbjct: 31 VVLEARDRVGGR-----TYTLRNQKVKYVDLGGSYVGPTQNRILR 70
>1mgp_A Hypothetical protein TM841; two domain structure with mixed
alpha/beta structures in BOTH domains, structural
genomics; HET: PLM; 2.00A {Thermotoga maritima} SCOP:
c.119.1.1 PDB: 1vpv_A*
Length = 313
Score = 25.3 bits (56), Expect = 7.5
Identities = 6/48 (12%), Positives = 15/48 (31%), Gaps = 12/48 (25%)
Query: 3 ATDVASKGLDFEEIKHVIN----------YDMPDDVENYVH--RIGRT 38
A ++ G EE+ ++ + + V R+ +
Sbjct: 157 AREMLENGATIEEVLKKLDERMKNKDFKAIFYVSNFDYLVKGGRVSKF 204
>2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing,
hydrolase, endonu nuclease; 2.85A {Escherichia coli}
PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A
Length = 517
Score = 25.3 bits (56), Expect = 8.7
Identities = 13/45 (28%), Positives = 15/45 (33%), Gaps = 13/45 (28%)
Query: 67 LLE-ARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITA 110
LLE +RQR+ P L E C C G G
Sbjct: 391 LLEMSRQRLSPSLGESSHHV------------CPRCSGTGTVRDN 423
>2jmk_A Hypothetical protein TA0956; protein binding; NMR {Thermoplasma
acidophilum} PDB: 2k24_A
Length = 111
Score = 24.4 bits (52), Expect = 9.9
Identities = 9/34 (26%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 6 VASKGLD-FEEIKHVINYDMPDDVENYVHRIGRT 38
V + L+ F E+ +I+ + D + +++ R RT
Sbjct: 23 VMDRFLESFSELYDIIDENDTDVMMDFISRFART 56
>2dt8_A DEGV family protein; fatty acid binding, structural genomics,
NPPSFA, natio project on protein structural and
functional analyses; HET: PLM; 1.48A {Thermus
thermophilus}
Length = 280
Score = 24.9 bits (55), Expect = 10.0
Identities = 7/48 (14%), Positives = 14/48 (29%), Gaps = 10/48 (20%)
Query: 1 MVATDVASKGLDFEEIKHVIN--------YDMPDDVENYVH--RIGRT 38
+ A ++ +G E + + +E RIG
Sbjct: 127 LRAKELLEEGQSLEAVLAELERLRRDHFVRFSVATLEFLKRGGRIGGA 174
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.136 0.392
Gapped
Lambda K H
0.267 0.0443 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,091,548
Number of extensions: 116026
Number of successful extensions: 435
Number of sequences better than 10.0: 1
Number of HSP's gapped: 421
Number of HSP's successfully gapped: 87
Length of query: 138
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 54
Effective length of database: 4,356,429
Effective search space: 235247166
Effective search space used: 235247166
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.5 bits)