RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7788
(115 letters)
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 83.8 bits (208), Expect = 8e-22
Identities = 34/49 (69%), Positives = 40/49 (81%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELES 60
IGRTG SG TG+ATTFINK+ DESVL+DLK LLLEA+Q++PP L L
Sbjct: 142 IGRTGCSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQVLHC 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 = 76.5 bits (189), Expect = 6e-19
Identities = 23/50 (46%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESE 61
IGRTGR G GLAT+F N+ + ++ DL LL+EA+Q +P +L + E
Sbjct: 134 IGRTGRVGNLGLATSFFNE-RNINITKDLLDLLVEAKQEVPSWLENMAYE 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 = 73.7 bits (182), Expect = 6e-17
Identities = 23/50 (46%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESE 61
IGRTGR G GLAT+F N+ + ++ DL LL+EA+Q +P +L + E
Sbjct: 364 IGRTGRVGNLGLATSFFNE-RNINITKDLLDLLVEAKQEVPSWLENMAYE 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 = 72.6 bits (179), Expect = 1e-16
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFL 55
IGRTGR G G AT+F + D ++ DL +L + Q +P FL
Sbjct: 388 IGRTGRVGNNGRATSFFDPEKDRAIAADLVKILEGSGQTVPDFL 431
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 42.5 bits (101), Expect = 6e-06
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRI----PPFLAELE 59
IGRTGR G+ G++ F++ + ++ ++ I ELE
Sbjct: 451 IGRTGRFGRVGVSINFVHDKKSWEEMNAIQEYF---QRPITRVPTDDYEELE 499
>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 = 42.2 bits (100), Expect = 7e-06
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESET 62
+ R GR G GLA TF++ ND +L D++ I E++ +
Sbjct: 338 VARAGRFGTKGLAITFVSDENDAKILNDVQDRF---EVNISELPDEIDISS 385
>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 = 41.0 bits (97), Expect = 1e-05
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESET 62
+ R GR G GLA TF++ ND +L D++ I E++ +
Sbjct: 119 VARAGRFGTKGLAITFVSDENDAKILNDVQDRF---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 = 40.2 bits (94), Expect = 4e-05
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLL--LEARQRIPPFLAELESETEKFLD 67
IGRT RSGK G + FI K + + +L+ + A+Q E++SE + +
Sbjct: 430 IGRTARSGKEGSSVLFICKD-ELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVT 486
>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 = 40.2 bits (95), Expect = 4e-05
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDL-KHLLLEARQRIPPFLAELESETEK 64
IGRTGR G+ G+A +F++ N ++L + K+ R+P + + K
Sbjct: 337 IGRTGRFGRKGVAISFVHDKNSFNILSAIQKYFGDIEMTRVPTDDWDEVEKIVK 390
>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 = 39.9 bits (94), Expect = 5e-05
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEK 64
IGR+GR G GLA I ND L ++ L IP + + E
Sbjct: 346 IGRSGRFGHLGLAINLI-NWNDRFNLYKIEQELGTEIAAIPATIDKSLYVAEN 397
>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 = 39.4 bits (92), Expect = 8e-05
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHL--LLEARQRIPPFLAELESETEKFLD 67
IGRT RSGK G + FI K + + +L+ ++ A+Q E++SE + +
Sbjct: 379 IGRTARSGKEGSSVLFICKD-ELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVT 435
>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 = 38.7 bits (91), Expect = 9e-05
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLL-DLKHLLLEARQRIPP-FLAELE 59
IGRT R+G+ G A + + + +LL + + + I + EL
Sbjct: 118 IGRTARAGRKGTAISLV--EAHDHLLLGKVGRYI---EEPIKARVIDELR 162
>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 = 38.7 bits (91), Expect = 1e-04
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDL-KHLLLEARQRIPPFLAELE 59
IGRTGR GK GLA I ++ L+ + H +Q + E+E
Sbjct: 128 IGRTGRFGKKGLAFNMIEV-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 = 39.2 bits (92), Expect = 1e-04
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 7/52 (13%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRI----PPFLAELE 59
IGRTGR GK GLA ++ + ++L ++ ++I L E+E
Sbjct: 427 IGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHF---NKKIERLDTDDLDEIE 475
>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 = 39.1 bits (92), Expect = 1e-04
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 7/52 (13%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRI----PPFLAELE 59
IGRTGR GK GLA ++ + ++L ++ ++I L E+E
Sbjct: 360 IGRTGRFGKRGLAVNMVDSKHSMNILNRIQEHF---NKKIERLDTDDLDEIE 408
>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase;
1.95A {Bacillus subtilis}
Length = 163
Score = 38.3 bits (90), Expect = 1e-04
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPP 53
GRTGR+G G A +F+ + ++ L D++ I
Sbjct: 123 TGRTGRAGNKGKAISFV-TAFEKRFLADIEEY---IGFEIQK 160
>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 = 37.9 bits (89), Expect = 2e-04
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 12 IGRTGRSGKTGLATTFIN 29
IGRTGR+GK G A + IN
Sbjct: 326 IGRTGRAGKKGKAISIIN 343
>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 = 37.9 bits (89), Expect = 2e-04
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPP 53
IGR+GR G+ G+A F+ K++D +L D++ +I
Sbjct: 364 IGRSGRYGRKGVAINFV-KNDDIRILRDIEQYY---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 = 37.5 bits (88), Expect = 3e-04
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPP 53
IGR GR G+ G+A + D+ L D++ I
Sbjct: 368 IGRGGRFGRKGVAINMV-TEEDKRTLRDIETFY---NTSIEE 405
>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 = 37.4 bits (87), Expect = 3e-04
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 9/61 (14%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRI----PPFLAEL-ESETEKFL 66
GRTGR+G+ G + + L+ +R PP E+ E++ L
Sbjct: 116 SGRTGRAGRGGRVVLLYG-PRERRDVEALERA---VGRRFKRVNPPTPEEVLEAKWRHLL 171
Query: 67 D 67
Sbjct: 172 A 172
>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 = 37.5 bits (88), Expect = 3e-04
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAEL 58
IGR GR G+ G+A F+ + D + +L+ + +P +A L
Sbjct: 347 IGRGGRFGRKGVAINFV-TNEDVGAMRELEKFYSTQIEELPSDIATL 392
>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 = 37.3 bits (87), Expect = 4e-04
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 9/61 (14%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRI----PPFLAEL-ESETEKFL 66
GRTGR+G+ G + + L+ +R PP E+ E++ L
Sbjct: 119 SGRTGRAGRGGRVVLLYG-PRERRDVEALERA---VGRRFKRVNPPTPEEVLEAKWRHLL 174
Query: 67 D 67
Sbjct: 175 A 175
>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein,
translation; 1.75A {Saccharomyces cerevisiae} SCOP:
c.37.1.19
Length = 165
Score = 36.4 bits (85), Expect = 5e-04
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELES 60
IGR GR G+ G+A F+ + D + +L+ + +P +A L +
Sbjct: 118 IGRGGRFGRKGVAINFV-TNEDVGAMRELEKFYSTQIEELPSDIATLLN 165
>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 = 36.3 bits (85), Expect = 8e-04
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 12 IGRTGRSGKTGLATTFINKSNDESVLLDLKHL 43
IGRTGR G+ G A TFI N+ + ++K +
Sbjct: 304 IGRTGRMGRKGEAITFI--LNEYWLEKEVKKV 333
>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 = 33.5 bits (76), Expect = 0.009
Identities = 15/51 (29%), Positives = 23/51 (45%)
Query: 17 RSGKTGLATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLD 67
R+GK+ + IN+ N + LDL+ FL EL+ E K +
Sbjct: 40 RTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVK 90
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 32.0 bits (73), Expect = 0.026
Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 2/58 (3%)
Query: 12 IGRTGRSGKTGL--ATTFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLD 67
GR+ R L + I + ++E LLL A + I E ++
Sbjct: 342 SGRSSRILNGVLVKGVSVIFEEDEEIFESLKTRLLLIAEEEIIEEAEANWKELVHEVE 399
>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 = 31.4 bits (70), Expect = 0.051
Identities = 16/85 (18%), Positives = 29/85 (34%), Gaps = 33/85 (38%)
Query: 11 MIGRTGRSGKTGLAT-------------------TFINKSNDESVLLDLKHLLL------ 45
++G SGKT +A N ++ E+VL L+ LL
Sbjct: 158 VLG----SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNW 213
Query: 46 ----EARQRIPPFLAELESETEKFL 66
+ I + +++E + L
Sbjct: 214 TSRSDHSSNIKLRIHSIQAELRRLL 238
>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 = 0.20
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 67 DLGGDERGCAYCGGLGHRITACP 89
L + C +C + H + +CP
Sbjct: 114 KLPPQPKKCHFCQSINHMVASCP 136
>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 = 0.25
Identities = 9/16 (56%), Positives = 9/16 (56%)
Query: 75 CAYCGGLGHRITACPK 90
CAYC GH CPK
Sbjct: 26 CAYCKEKGHWAKDCPK 41
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding,
exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Length = 124
Score = 28.2 bits (62), Expect = 0.40
Identities = 7/22 (31%), Positives = 8/22 (36%)
Query: 69 GGDERGCAYCGGLGHRITACPK 90
C CGG GH C +
Sbjct: 102 PFHTIYCYNCGGKGHFGDDCKE 123
Score = 25.5 bits (55), Expect = 3.4
Identities = 6/16 (37%), Positives = 6/16 (37%)
Query: 75 CAYCGGLGHRITACPK 90
C C GH CP
Sbjct: 7 CNNCSQRGHLKKDCPH 22
>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA,
transcription-RNA complex; NMR {Homo sapiens}
Length = 74
Score = 27.3 bits (60), Expect = 0.54
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 73 RGCAYCGGLGHRITACPK 90
+ C +C + H + +CP
Sbjct: 47 KKCHFCQSISHMVASCPL 64
>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 = 26.3 bits (57), Expect = 0.54
Identities = 10/21 (47%), Positives = 10/21 (47%)
Query: 71 DERGCAYCGGLGHRITACPKL 91
D CAYC GH CPK
Sbjct: 9 DRDQCAYCKEKGHWAKDCPKK 29
>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 = 26.8 bits (59), Expect = 0.62
Identities = 5/18 (27%), Positives = 10/18 (55%)
Query: 73 RGCAYCGGLGHRITACPK 90
+ C +C + H + +CP
Sbjct: 30 KKCHFCQSISHMVASCPL 47
Score = 24.9 bits (54), Expect = 3.2
Identities = 8/22 (36%), Positives = 8/22 (36%)
Query: 69 GGDERGCAYCGGLGHRITACPK 90
G C CGGL H C
Sbjct: 4 GSSGDRCYNCGGLDHHAKECKL 25
>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 = 0.74
Identities = 5/17 (29%), Positives = 6/17 (35%)
Query: 75 CAYCGGLGHRITACPKL 91
C C H CP +
Sbjct: 8 CTLCKSKKHSKERCPSI 24
Score = 26.5 bits (58), Expect = 1.1
Identities = 10/37 (27%), Positives = 15/37 (40%)
Query: 54 FLAELESETEKFLDLGGDERGCAYCGGLGHRITACPK 90
++ ++E K L C CGG GH C +
Sbjct: 28 YILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKE 64
>2a51_A Nucleocapsid protein; sivlhoest, structure, NCP8, viral protein,
metal binding protein; NMR {Synthetic}
Length = 39
Score = 26.0 bits (57), Expect = 0.80
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 72 ERGCAYCGGLGHRITACPK 90
+ GC CG HR CPK
Sbjct: 21 QEGCWNCGSKEHRFAQCPK 39
>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 = 27.5 bits (62), Expect = 0.94
Identities = 10/48 (20%), Positives = 12/48 (25%), Gaps = 7/48 (14%)
Query: 59 ESETEKFLDLGGD-------ERGCAYCGGLGHRITACPKLEAVQTKAA 99
ESE E G G + EA+ T A
Sbjct: 185 ESEAELLQPYGVKTLVITQGAAGAWLVQEGQRQFCPAVPAEALDTTGA 232
>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 = 27.6 bits (61), Expect = 0.95
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 77 YCGGLGHRITACPKLEAVQTKAASSIGR 104
Y G+GH +T P L A +++ +IGR
Sbjct: 39 YTIGIGHLLTKSPSLNAAKSELDKAIGR 66
>2ihx_A Nucleocapsid (NC) protein; protein-RNA complex, viral protein/RNA
complex; NMR {Rous sarcoma virus}
Length = 61
Score = 25.6 bits (56), Expect = 1.4
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 69 GGDERGCAYCGGLGHRITACPK 90
G C C G+GH C K
Sbjct: 27 GNSRERCQLCNGMGHNAKQCRK 48
>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 = 24.9 bits (54), Expect = 2.1
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 72 ERGCAYCGGLGHRITACPKLEA 93
+GC CG GH + CP+ +A
Sbjct: 27 RQGCWKCGKTGHVMAKCPERQA 48
>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 = 26.5 bits (58), Expect = 2.2
Identities = 6/37 (16%), Positives = 14/37 (37%)
Query: 28 INKSNDESVLLDLKHLLLEARQRIPPFLAELESETEK 64
+ S E +++D K + ++ + E K
Sbjct: 235 VKLSEAEYIIIDEKSVNSAVKKIVNEAAEVAGVEVLK 271
>2nlr_A CELB, protein (endoglucanase (E.C.3.2.1.4)); hydrolase
(endoglucanase), glycosyl hydrolase, family 12,
glycosyl-enzyme intermediate; HET: BGC G2F SHG; 1.20A
{Streptomyces lividans} SCOP: b.29.1.11 PDB: 1nlr_A
1oa4_A
Length = 234
Score = 26.1 bits (57), Expect = 2.5
Identities = 7/44 (15%), Positives = 16/44 (36%), Gaps = 4/44 (9%)
Query: 26 TFINKSNDESVLLDLKHLL--LEARQRIPP--FLAELESETEKF 65
+F+ S D+ + AR +L +++ E +
Sbjct: 162 SFVAPSAISGWSFDVMDFVRATVARGLAENDWYLTSVQAGFEPW 205
>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 = 26.0 bits (58), Expect = 3.7
Identities = 13/45 (28%), Positives = 15/45 (33%), Gaps = 13/45 (28%)
Query: 44 LLE-ARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITA 87
LLE +RQR+ P L E C C G G
Sbjct: 391 LLEMSRQRLSPSLGESSHHV------------CPRCSGTGTVRDN 423
>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 = 26.0 bits (57), Expect = 3.7
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 5/45 (11%)
Query: 43 LLLEARQRIPPFLAELESETEKFLDLGGDERGCAYCGGLGHRITA 87
++LEAR R+ + T + + + G +Y G +RI
Sbjct: 31 VVLEARDRVGGR-----TYTLRNQKVKYVDLGGSYVGPTQNRILR 70
>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 = 24.0 bits (52), Expect = 4.3
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 75 CAYCGGLGHRITACP 89
C CG GH I CP
Sbjct: 10 CFRCGKPGHYIKNCP 24
>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 = 24.1 bits (52), Expect = 5.2
Identities = 6/29 (20%), Positives = 8/29 (27%)
Query: 73 RGCAYCGGLGHRITACPKLEAVQTKAASS 101
C CG GH C + +
Sbjct: 2 GSCFKCGKKGHFAKNCHEHAHNNAEPKVP 30
>2amy_A PMM 2, phosphomannomutase 2; HS.459855, HS.313504, BC008310,
phosphatase, PFAM PF03332, H superfamily, jaecken
disease; 2.09A {Homo sapiens} SCOP: c.108.1.10 PDB:
2q4r_A
Length = 246
Score = 25.3 bits (54), Expect = 6.1
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 4/40 (10%)
Query: 36 VLLDLKHLLLEARQRIPP----FLAELESETEKFLDLGGD 71
L D+ L RQ+I FL +L + + + G D
Sbjct: 9 CLFDVDGTLTAPRQKITKEMDDFLQKLRQKIKIGVVGGSD 48
>2pz1_A RHO guanine nucleotide exchange factor 4; helical bundle, beta
barrel, beta sandwich, signaling protei; 2.25A {Homo
sapiens} PDB: 2dx1_A 3nmz_D 3nmx_D
Length = 466
Score = 25.3 bits (55), Expect = 6.7
Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 38 LDLKHLLLEARQRI---PPFLAELESETEK 64
+ L LL Q+I P LAEL T
Sbjct: 248 ISLDGFLLTPVQKICKYPLQLAELLKYTHP 277
>3ry7_A Ribokinase; transferase; 2.15A {Staphylococcus aureus}
Length = 304
Score = 25.1 bits (56), Expect = 6.8
Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 7/52 (13%)
Query: 55 LAELESETEKFLDLGGD-------ERGCAYCGGLGHRITACPKLEAVQTKAA 99
++ FL +G ++G + + K+ A+ T AA
Sbjct: 201 EQSMKDNANYFLSIGIKTVLITLGKQGTYFATKNQSQHIEAYKVNAIDTTAA 252
>2z0q_A XPLN, RHO guanine nucleotide exchange factor 3; DH-PH domain,
alternative splicing, cytoplasm, guanine- nucleotide
releasing factor; 1.79A {Mus musculus} PDB: 3eo2_A
Length = 346
Score = 25.1 bits (55), Expect = 6.9
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 38 LDLKHLLLEARQRIP 52
LDL + L R R+
Sbjct: 147 LDLWNFLDIPRSRLV 161
>3jv3_A Intersectin-1; SH3 domain, DH domain, guanine nucleotide exchange
factor, autoinhibition, domain-swapped, cell junction,
cell project endocytosis; 2.40A {Mus musculus} PDB:
3gf9_A
Length = 283
Score = 24.7 bits (54), Expect = 7.5
Identities = 5/30 (16%), Positives = 13/30 (43%), Gaps = 3/30 (10%)
Query: 38 LDLKHLLLEARQRIPPF---LAELESETEK 64
+ L +L+ QR+ + + + T +
Sbjct: 214 MPLSSFILKPMQRVTRYPLIIKNILENTPE 243
>2dfk_A Collybistin II; DH domain, PH domain, cell cycle; 2.15A {Rattus
norvegicus} SCOP: a.87.1.1 b.55.1.1
Length = 402
Score = 24.8 bits (54), Expect = 7.6
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 3/30 (10%)
Query: 38 LDLKHLLLEARQRIP--PF-LAELESETEK 64
+ + LL Q+I P LAEL T +
Sbjct: 171 IAIDGFLLTPVQKICKYPLQLAELLKYTAQ 200
>2epl_X N-acetyl-beta-D-glucosaminidase; glycoside hydrolase, family 20,
GCNA, hydro; 1.40A {Streptococcus gordonii} PDB: 2epk_X
2epm_X 2epn_A* 2epo_A
Length = 627
Score = 25.0 bits (54), Expect = 7.6
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 8/57 (14%)
Query: 40 LKHLLLEARQRIPPFLA-------ELESETEKFLDLGGDERGCAYCGGLGHRI-TAC 88
L + A++R+ F++ ELE E F D D+ A H I TA
Sbjct: 566 LLKRIKRAQERLEQFISGQIDCVEELEQEILPFNDFYKDQGLTATTANQWHLIATAS 622
>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 = 23.4 bits (50), Expect = 7.7
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 72 ERGCAYCGGLGHRITACPKLEA 93
++GC CG GH++ C + +A
Sbjct: 33 KKGCWKCGKEGHQMKDCTERQA 54
>1vm7_A Ribokinase; TM0960, structural genomics, JCSG, protein struc
initiative, PSI, joint center for structural genomics,
TRAN; 2.15A {Thermotoga maritima} SCOP: c.72.1.1
Length = 311
Score = 24.8 bits (55), Expect = 8.1
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 7/52 (13%)
Query: 55 LAELESETEKFLDLGGD-------ERGCAYCGGLGHRITACPKLEAVQTKAA 99
+E EKFL+LG ++G + K++AV T AA
Sbjct: 205 FLTVEKAAEKFLELGVKNVIVKLGDKGVLLVNKNEKKHFPTFKVKAVDTTAA 256
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 24.7 bits (54), Expect = 8.5
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 11 MIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLL 45
M GR GR G + + + + E V K +L
Sbjct: 386 MSGRAGRPGFDQIGESIVVVRDKEDVDRVFKKYVL 420
>2ohf_A Protein OLA1, GTP-binding protein 9; ATPase, GTPase, P-loop,
OBG-like, hydrolase; HET: ACP; 2.70A {Homo sapiens}
Length = 396
Score = 24.7 bits (55), Expect = 8.6
Identities = 6/21 (28%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 55 LAELES-ETEKFLDLGGDERG 74
L EL + E +K+L+ +
Sbjct: 271 LQELSAEERQKYLEANMTQSA 291
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
0.318 0.134 0.388
Gapped
Lambda K H
0.267 0.0554 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,648,754
Number of extensions: 85512
Number of successful extensions: 275
Number of sequences better than 10.0: 1
Number of HSP's gapped: 273
Number of HSP's successfully gapped: 69
Length of query: 115
Length of database: 6,701,793
Length adjustment: 78
Effective length of query: 37
Effective length of database: 4,523,955
Effective search space: 167386335
Effective search space used: 167386335
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 (21.7 bits)
S2: 51 (23.8 bits)