RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10677
(317 letters)
>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding,
hydrolase, nucleotide- RNA-binding, methylation, mRNA
processing, mRNA S nucleus; HET: ADP; 2.60A {Homo
sapiens}
Length = 242
Score = 138 bits (350), Expect = 1e-39
Identities = 59/167 (35%), Positives = 85/167 (50%), Gaps = 25/167 (14%)
Query: 110 TKEEIDSFRKEHNITLIGQNIPKPVKTLDETNIPSYILGPMKPKTTNNENNHNKNKKCGD 169
T +E++++R+ IT+ G N PKPV E N P+ ++ +
Sbjct: 4 TAQEVETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIA------------------ 45
Query: 170 KESKNWTIPLNFQAKKFISVLQKK-----AEVQSRSVFTYILPALYHILKMPKLEEGDGP 224
+N+T P QA+ + L A+ S +Y+LPA+ HI P LE GDGP
Sbjct: 46 --RQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFLERGDGP 103
Query: 225 IALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
I LVLAPTRELAQQ+Q V + + R R++ C+YGG K Q+ L
Sbjct: 104 ICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIRDLE 150
Score = 67.6 bits (166), Expect = 2e-13
Identities = 17/31 (54%), Positives = 26/31 (83%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANL 31
MWSATWP+E+++LA++FL D I +N+G+ L
Sbjct: 212 MWSATWPKEVRQLAEDFLKDYIHINIGALEL 242
>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 = 116 bits (294), Expect = 7e-30
Identities = 40/185 (21%), Positives = 70/185 (37%), Gaps = 29/185 (15%)
Query: 95 VPSYPDPSVNHLQGKTKEEIDSFRKEHNI--TLIGQNIPKPVKTLDETNIPSYILGPMKP 152
+P P + F K +NI + G ++P+P++ ++ I+
Sbjct: 14 IPPEPSNDAIEIFSSGIASGIHFSKYNNIPVKVTGSDVPQPIQHFTSADLRDIII----- 68
Query: 153 KTTNNENNHNKN-KKCGDKESKNWTIPLNFQAKKFISVLQKK-----AEVQSRSVFTYIL 206
N K G + IP Q + + A+ S ++L
Sbjct: 69 ----------DNVNKSG------YKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLL 112
Query: 207 PALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQ 266
P L +L+ P E P ++++PTRELA QI F+ ++ +YGGTS +Q
Sbjct: 113 PILSKLLEDPHELELGRPQVVIVSPTRELAIQIFNEARKFAFESYLKIGIVYGGTSFRHQ 172
Query: 267 VILLR 271
+
Sbjct: 173 NECIT 177
Score = 88.8 bits (221), Expect = 6e-20
Identities = 19/52 (36%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEKPAK 52
M+SAT+P EIQ++A EFL + + + +G A ++KQ + ++Y K +K
Sbjct: 241 MFSATFPEEIQRMAGEFLKNYVFVAIGIVG-GACSDVKQTIYEVNKYAKRSK 291
>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural
genomics, structural GEN consortium, SGC, rRNA,
ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}
Length = 245
Score = 98.8 bits (247), Expect = 1e-24
Identities = 34/165 (20%), Positives = 61/165 (36%), Gaps = 35/165 (21%)
Query: 112 EEIDSFRKEHNITLIGQNIPKPVKTLDET----NIPSYILGPMKPKTTNNENNHNKN-KK 166
+I+ R +H I + G ++P P+ T + I S +L +N
Sbjct: 2 MKINFLRNKHKIHVQGTDLPDPIATFQQLDQEYKINSRLL---------------QNILD 46
Query: 167 CGDKESKNWTIPLNFQAKKFISVLQKK---AEVQSRSVFT--YILPALYHILKMPKLEEG 221
G + +P Q + +L + A + S T + +P L + +
Sbjct: 47 AG------FQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA----N 96
Query: 222 DGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQ 266
G AL+++PTRELA QI + S R ++ +
Sbjct: 97 KGFRALIISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKK 141
Score = 59.9 bits (146), Expect = 1e-10
Identities = 9/30 (30%), Positives = 20/30 (66%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSAN 30
M+SAT+ ++++ K L + I +++G+ N
Sbjct: 215 MFSATFAYDVEQWCKLNLDNVISVSIGARN 244
>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC,
structural GE consortium, hydrolase; HET: AMP; 2.20A
{Homo sapiens}
Length = 417
Score = 99 bits (250), Expect = 6e-24
Identities = 39/175 (22%), Positives = 58/175 (33%), Gaps = 54/175 (30%)
Query: 123 ITLIGQNIPKPVKTLDETNIPSYILGPMKPKTTNNENNHNKN-KKCGDKESKNWTIPLNF 181
+ G N P +++ + + I+ N + +T P
Sbjct: 3 VEATGNNCPPHIESFSDVEMGEIIM---------------GNIELTR------YTRPTPV 41
Query: 182 QAKKFISVLQKK-----AEVQSRSVFT-------YILPALYHILKMPKLE---------- 219
Q + +K+ A+ T ++LP L I E
Sbjct: 42 QKHAIPIIKEKRDLMACAQ-------TGSGKTAAFLLPILSQIYSDGPGEALRAMKENGR 94
Query: 220 ---EGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
PI+LVLAPTRELA QI FS R+R +YGG Q+ L
Sbjct: 95 YGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVVYGGADIGQQIRDLE 149
Score = 88.0 bits (219), Expect = 9e-20
Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEKPAK 52
M+SAT+P+EIQ LA++FL + I L VG + + NI Q V E +K +
Sbjct: 215 MFSATFPKEIQMLARDFLDEYIFLAVGRVG-STSENITQKVVWVEESDKRSF 265
>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX,
structural genomics, structural genomi consortium, SGC,
ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}
Length = 228
Score = 94.2 bits (235), Expect = 4e-23
Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 204 YILPALYHILKMPK-LEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTS 262
Y++P H+ P E+ +GP LVL PTRELA ++A S +S ++ C+YGG +
Sbjct: 74 YLMPGFIHLDSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYK-GLKSICIYGGRN 132
Query: 263 KMYQVILLR 271
+ Q+ +
Sbjct: 133 RNGQIEDIS 141
Score = 58.0 bits (141), Expect = 4e-10
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNV 26
M SATWP +++LA +L DP+ + V
Sbjct: 203 MTSATWPDTVRQLALSYLKDPMIVYV 228
>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA,
N project on protein structural and functional analyses;
2.40A {Dugesia japonica} SCOP: c.37.1.19
Length = 253
Score = 92.2 bits (230), Expect = 4e-22
Identities = 33/164 (20%), Positives = 61/164 (37%), Gaps = 33/164 (20%)
Query: 120 EHNITLIGQNI--PKPVKTLDETNIPSYILGPMKPKTTNNENNHNKN-KKCGDKESKNWT 176
+++ G + ++ DE + I N +
Sbjct: 6 SIPVSVTGPDYSATNVIENFDELKLDPTIR---------------NNILLAS------YQ 44
Query: 177 IPLNFQAKKFISVLQKK---AEVQSRSVFT--YILPALYHILK----MPKLEEGDGPIAL 227
P Q ++L+ + A Q+ S T +++P + H++ + + P L
Sbjct: 45 RPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTAYPKCL 104
Query: 228 VLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
+LAPTRELA QI + FS +R +YGG Q+ ++
Sbjct: 105 ILAPTRELAIQILSESQKFSLNTPLRSCVVYGGADTHSQIREVQ 148
Score = 75.3 bits (186), Expect = 4e-16
Identities = 19/41 (46%), Positives = 29/41 (70%), Gaps = 1/41 (2%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFV 41
M+SAT+P+EIQKLA +FL + I + VG + + +IKQ +
Sbjct: 214 MFSATFPKEIQKLAADFLYNYIFMTVGRVG-STSDSIKQEI 253
>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural
genomics, structural GEN consortium, SGC, ATP-binding,
hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}
Length = 249
Score = 65.8 bits (161), Expect = 1e-12
Identities = 23/68 (33%), Positives = 33/68 (48%), Gaps = 5/68 (7%)
Query: 204 YILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSK 263
+ LP L +L+ P+ ALVL PTRELA QI ++ ++ A + GG
Sbjct: 97 FALPILNALLETPQ-----RLFALVLTPTRELAFQISEQFEALGSSIGVQSAVIVGGIDS 151
Query: 264 MYQVILLR 271
M Q + L
Sbjct: 152 MSQSLALA 159
Score = 38.1 bits (89), Expect = 0.002
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGS 28
SAT +++QKL + L +P++ V S
Sbjct: 224 SATMTKKVQKLQRAALKNPVKCAVSS 249
>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural
genomics, structural genomic consortium, SGC, hydrolase;
HET: ADP; 2.15A {Homo sapiens}
Length = 236
Score = 65.0 bits (159), Expect = 2e-12
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 1/68 (1%)
Query: 204 YILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSK 263
+++P L L + DG L+++PTRELA Q V+ + + GG
Sbjct: 79 FLVPVL-EALYRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDL 137
Query: 264 MYQVILLR 271
++ +
Sbjct: 138 KHEAERIN 145
Score = 34.5 bits (80), Expect = 0.024
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNV 26
SAT + ++ LA+ L +P + V
Sbjct: 209 SATQTKSVKDLARLSLKNPEYVWV 232
>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics,
structural genomics consort ATP-binding, hydrolase,
nucleotide-binding, RNA-B; 2.80A {Homo sapiens}
Length = 262
Score = 61.6 bits (150), Expect = 3e-11
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 204 YILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSK 263
+++PA+ ++ + +G L+L+PTRELA Q V+ + + GG+++
Sbjct: 108 FLIPAV-ELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNR 166
Query: 264 MYQVILLR 271
+ L
Sbjct: 167 SAEAQKLG 174
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 61.3 bits (149), Expect = 9e-11
Identities = 10/72 (13%), Positives = 24/72 (33%), Gaps = 9/72 (12%)
Query: 204 YILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSK 263
++ AL+ K G + ++ PT L +Q + + +++ Y K
Sbjct: 53 GMMTALWLARK--------GKKSALVFPTVTLVKQTLERLQKLADE-KVKIFGFYSSMKK 103
Query: 264 MYQVILLRILTS 275
+ +
Sbjct: 104 EEKEKFEKSFEE 115
Score = 41.3 bits (97), Expect = 3e-04
Identities = 11/74 (14%), Positives = 16/74 (21%), Gaps = 22/74 (29%)
Query: 1 MWSATWPREIQKLAKE---------------------FLSDPIQLNVGSANLAANPNIKQ 39
+S +I + K D + VG A NI
Sbjct: 175 AFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVA-RNITH 233
Query: 40 FVEICHEYEKPAKW 53
EK +
Sbjct: 234 VRISSRSKEKLVEL 247
>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family,
gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP:
c.37.1.19 PDB: 1qva_A
Length = 224
Score = 59.9 bits (146), Expect = 9e-11
Identities = 22/46 (47%), Positives = 27/46 (58%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
AL+LAPTRELA QIQ V+ + M I+ GGTS + LR
Sbjct: 85 ALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR 130
Score = 36.8 bits (86), Expect = 0.006
Identities = 8/29 (27%), Positives = 18/29 (62%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSANL 31
SAT P ++ ++ +F+ +P+++ V L
Sbjct: 193 SATMPNDVLEVTTKFMRNPVRILVKKDEL 221
>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX,
structural genomics, helic binding, HOST-virus
interaction, hydrolase; 1.85A {Homo sapiens} PDB:
2g9n_A*
Length = 237
Score = 58.8 bits (143), Expect = 3e-10
Identities = 22/46 (47%), Positives = 26/46 (56%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
ALVLAPTRELAQQIQ VI M GGT+ ++ L+
Sbjct: 101 ALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQ 146
Score = 36.0 bits (84), Expect = 0.009
Identities = 10/24 (41%), Positives = 18/24 (75%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNV 26
SAT P ++ ++ K+F+ DPI++ V
Sbjct: 211 SATMPTDVLEVTKKFMRDPIRILV 234
>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 = 59.9 bits (146), Expect = 3e-10
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 7/70 (10%)
Query: 203 TYILPALYHILKMPKLEEGDGPI-ALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGT 261
+++P L K++ I AL++ PTRELA Q V+ + I GGT
Sbjct: 74 AFVIPTL------EKVKPKLNKIQALIMVPTRELALQTSQVVRTLGKHCGISCMVTTGGT 127
Query: 262 SKMYQVILLR 271
+ ++ L
Sbjct: 128 NLRDDILRLN 137
Score = 44.1 bits (105), Expect = 4e-05
Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEK 49
++SAT+P +++ + L P ++N+ L I Q+ E +K
Sbjct: 199 LFSATFPLTVKEFMVKHLHKPYEINL-MEELTL-KGITQYYAFVEERQK 245
>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 = 59.5 bits (145), Expect = 3e-10
Identities = 22/46 (47%), Positives = 27/46 (58%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
AL+LAPTRELA QIQ V+ + M I+ GGTS + LR
Sbjct: 92 ALMLAPTRELALQIQKVVMALAFHMDIKVHACIGGTSFVEDAEGLR 137
Score = 44.4 bits (106), Expect = 3e-05
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF-VEICHEYEK 49
SAT P ++ ++ +F+ +P+++ V L IKQF V + E K
Sbjct: 200 SATMPNDVLEVTTKFMRNPVRILVKKDELTL-EGIKQFYVNVEEEEYK 246
>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 = 59.1 bits (144), Expect = 5e-10
Identities = 22/46 (47%), Positives = 26/46 (56%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
ALVLAPTRELAQQIQ V+ M GGT+ +V L+
Sbjct: 111 ALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQKLQ 156
Score = 46.4 bits (111), Expect = 6e-06
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF-VEICHEYEK 49
SAT P ++ ++ K+F+ DPI++ V L I+QF + + E K
Sbjct: 221 SATMPSDVLEVTKKFMRDPIRILVKKEELTL-EGIRQFYINVEREEWK 267
>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 = 58.7 bits (143), Expect = 6e-10
Identities = 18/46 (39%), Positives = 24/46 (52%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
AL+LAPTRELA QIQ + M ++ GGT+ + L
Sbjct: 108 ALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLD 153
Score = 47.2 bits (113), Expect = 3e-06
Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF-VEICHEYEK 49
SAT P EI ++ +F++DPI++ V L IKQF V + E K
Sbjct: 217 SATLPHEILEMTNKFMTDPIRILVKRDELTL-EGIKQFFVAVEREEWK 263
>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 = 57.5 bits (140), Expect = 2e-09
Identities = 18/55 (32%), Positives = 29/55 (52%)
Query: 217 KLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
+ E +G A++L PTRELA Q+ I ++ A +YGG + Q+ L+
Sbjct: 68 LVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK 122
Score = 46.0 bits (110), Expect = 7e-06
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEK 49
SAT PREI LAK+++ D + N NI+Q +E E+
Sbjct: 185 SATMPREILNLAKKYMGDYSFIKA-----KINANIEQSYVEVNENER 226
>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 = 57.6 bits (140), Expect = 2e-09
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIR-HACLYGGTSKMYQV 267
A+ LAP+RELA+Q V+ + +I + K Q+
Sbjct: 78 AICLAPSRELARQTLEVVQEMGKFTKITSQLIVPDSFEKNKQI 120
Score = 45.2 bits (108), Expect = 1e-05
Identities = 11/48 (22%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF-VEICHEYEK 49
SAT+ +++ AK+ + + L + + + IKQ ++ +E +K
Sbjct: 184 SATFADAVRQYAKKIVPNANTLELQTNEVNV-DAIKQLYMDCKNEADK 230
>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 = 56.4 bits (137), Expect = 3e-09
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLR 271
+LV+ PTREL +Q+ + I R M + A +YGG Q+ +R
Sbjct: 59 SLVVTPTRELTRQVASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR 104
Score = 42.5 bits (101), Expect = 9e-05
Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEK 49
++SAT P EI+K+ K+F+++ ++ N++ + +
Sbjct: 165 LFSATIPEEIRKVVKDFITNYEEIEACI----GLANVEHKFVHVKDDWR 209
>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 = 56.7 bits (137), Expect = 3e-09
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 204 YILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSR----TMRIRHACLYG 259
+++P H++ K + A+++APTR+LA QI+A + + L G
Sbjct: 77 FLIPIFQHLINT-KFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVG 135
Query: 260 GTSKMYQVILLR 271
GT + +
Sbjct: 136 GTDFRAAMNKMN 147
Score = 46.0 bits (109), Expect = 1e-05
Identities = 13/52 (25%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANL---AANPNIKQFVEICHEYEK 49
++SAT ++QKLA ++ L + + + A+ I Q V I ++
Sbjct: 218 LFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFAN 269
>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 = 56.7 bits (137), Expect = 3e-09
Identities = 17/70 (24%), Positives = 30/70 (42%), Gaps = 5/70 (7%)
Query: 206 LPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSR----TMRIRHACLYGGT 261
+P H++ K + A+++APTR+LA QI+A + + L GGT
Sbjct: 130 IPIFQHLINT-KFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGT 188
Query: 262 SKMYQVILLR 271
+ +
Sbjct: 189 DFRAAMNKMN 198
Score = 45.2 bits (107), Expect = 2e-05
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSANL---AANPNIKQFVEICHEYEK 49
SAT ++QKLA ++ L + + + A+ I Q V I ++
Sbjct: 271 SATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFAN 320
>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase, translation
termination, binding, hydrolase, membrane, mRNA
transport; 2.80A {Schizosaccharomyces pombe}
Length = 508
Score = 56.4 bits (137), Expect = 5e-09
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 13/61 (21%)
Query: 203 TYILPALYHI---LKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYG 259
+ L L + + P+ A+ LAP+RELA+QI V++ + ++ +G
Sbjct: 174 AFALTMLSRVDASVPKPQ--------AICLAPSRELARQIMDVVTEMGKYTEVK--TAFG 223
Query: 260 G 260
Sbjct: 224 I 224
Score = 47.9 bits (115), Expect = 2e-06
Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF-VEICHEYEK 49
SAT+ ++K A+ F + ++ + + L+ IKQ ++ E K
Sbjct: 298 SATFSERVEKYAERFAPNANEIRLKTEELSV-EGIKQLYMDCQSEEHK 344
>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA
processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP:
c.37.1.19
Length = 220
Score = 54.2 bits (131), Expect = 7e-09
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 203 TYILPALYHILKMPKLEEGDGPI-ALVLAPTRELAQQIQAVISIFSRTMR-IRHACLYGG 260
++L L +LE G + LV+ TRELA QI FS+ M ++ A +GG
Sbjct: 67 VFVLATL------QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGG 120
Query: 261 TSKMYQVILLR 271
S +L+
Sbjct: 121 LSIKKDEEVLK 131
Score = 37.6 bits (88), Expect = 0.003
Identities = 10/26 (38%), Positives = 20/26 (76%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNV 26
M+SAT +EI+ + ++F+ DP+++ V
Sbjct: 195 MFSATLSKEIRPVCRKFMQDPMEIFV 220
>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural
genomics, structural genomics consortium, SGC,
hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*
Length = 230
Score = 54.2 bits (131), Expect = 8e-09
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMR-IRHACLYGGTSKMYQVILLR 271
L+LAPTRE+A QI +VI+ M + GGT L+
Sbjct: 95 ILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK 141
Score = 36.8 bits (86), Expect = 0.004
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGS 28
SAT+P + +++ DP + + S
Sbjct: 203 AVSATYPEFLANALTKYMRDPTFVRLNS 230
>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic
resolution, AMP complex, ribosome biogenesis,
thermophilic, hydrolase; HET: AMP; 1.20A {Thermus
thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A*
3mwl_A* 3nbf_A* 3nej_A
Length = 207
Score = 53.7 bits (130), Expect = 9e-09
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 206 LPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMY 265
LP + P E G P ALVL PTRELA Q+ + ++ + +++ +YGGT
Sbjct: 57 LPIAERL--APSQERGRKPRALVLTPTRELALQVASELTAVAPHLKV--VAVYGGTGYGK 112
Query: 266 QVILLR 271
Q L
Sbjct: 113 QKEALL 118
Score = 37.5 bits (88), Expect = 0.003
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNV 26
SAT P ++LA+ ++ +P+ +NV
Sbjct: 182 SATLPSWAKRLAERYMKNPVLINV 205
>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 = 54.5 bits (132), Expect = 1e-08
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 203 TYILPALYHILKMPKLEEGDGPI-ALVLAPTRELAQQIQAVISIFSRTMR-IRHACLYGG 260
++L L +LE G + LV+ TRELA QI FS+ M ++ A +GG
Sbjct: 61 VFVLATL------QQLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGG 114
Query: 261 TSKMYQVILLR 271
S +L+
Sbjct: 115 LSIKKDEEVLK 125
Score = 45.3 bits (108), Expect = 1e-05
Identities = 13/49 (26%), Positives = 27/49 (55%)
Query: 1 MWSATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQFVEICHEYEK 49
M+SAT +EI+ + ++F+ DP+++ V ++Q+ + EK
Sbjct: 189 MFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEK 237
>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding
protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19
Length = 206
Score = 52.9 bits (128), Expect = 2e-08
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 203 TYILPALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMR-IRHACLYGGT 261
Y++P L + + D A+V+ PTRELA Q+ + S+ M + GGT
Sbjct: 56 AYLIPLLERLD-----LKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGT 110
Query: 262 SKMYQVILLR 271
+ ++ L
Sbjct: 111 NLRDDIMRLD 120
Score = 36.0 bits (84), Expect = 0.009
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 3 SATWPREIQKLAKEFLSDPIQLN 25
SAT+P +QK L P ++N
Sbjct: 184 SATFPLSVQKFMNSHLEKPYEIN 206
>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus
stearothermophilus} SCOP: c.37.1.19
Length = 219
Score = 51.4 bits (124), Expect = 6e-08
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTM----RIRHACLYGGTSKMYQVILLR 271
A++ APTRELA QI ++ I CL GGT K + L
Sbjct: 75 AVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLN 124
Score = 37.9 bits (89), Expect = 0.002
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSAN 30
SAT P +++ K+++ +P ++V +
Sbjct: 188 SATIPEKLKPFLKKYMENPTFVHVLEHH 215
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 51.1 bits (123), Expect = 6e-08
Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 6/59 (10%)
Query: 16 EFLSDPIQLNVGSANL------AANPNIKQFVEICHEYEKPAKWWDSNNGHYPKSVRFV 68
+++G+ NL AA+ ++ Q VE E K + P + F
Sbjct: 3 HHHHHSSGVDLGTENLYFQSMGAASLDVIQEVEYVKEEAKMVYLLECLQKTPPPVLIFA 61
>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore
complex, nucleocytoplasmic trans mRNA export, protein
interaction, beta-propeller; HET: ADP; 2.51A {Homo
sapiens}
Length = 300
Score = 51.6 bits (124), Expect = 1e-07
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMR-IRHACLYGGTS 262
L L+PT ELA Q VI + ++ A G
Sbjct: 165 CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNK 202
Score = 34.3 bits (79), Expect = 0.036
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNV 26
SAT+ + K A++ + DP + +
Sbjct: 274 SATFEDSVWKFAQKVVPDPNVIKL 297
>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 = 51.8 bits (125), Expect = 1e-07
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMR-IRHACLYGGTS 262
L L+PT ELA Q VI + ++ A G
Sbjct: 98 CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNK 135
Score = 43.7 bits (104), Expect = 5e-05
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF-VEICHEYEK 49
SAT+ + K A++ + DP + + IKQ+ V EK
Sbjct: 207 SATFEDSVWKFAQKVVPDPNVIKLKREEETL-DTIKQYYVLCSSRDEK 253
>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 = 51.2 bits (123), Expect = 2e-07
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMR-IRHACLYGGTS 262
L L+PT ELA Q VI + ++ A G
Sbjct: 165 CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNK 202
Score = 42.7 bits (101), Expect = 1e-04
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 3 SATWPREIQKLAKEFLSDPIQLNVGSANLAANPNIKQF-VEICHEYEK 49
SAT+ + K A++ + DP + + IKQ+ V EK
Sbjct: 274 SATFEDSVWKFAQKVVPDPNVIKLKREEETL-DTIKQYYVLCSSRDEK 320
>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 = 43.3 bits (103), Expect = 2e-05
Identities = 7/33 (21%), Positives = 12/33 (36%), Gaps = 1/33 (3%)
Query: 20 DPIQLNVGSANLAANPNIKQFVEICHEYEKPAK 52
N+ + + NI Q V E +K +
Sbjct: 4 HHHHENLYFQ-GSTSENITQKVVWVEESDKRSF 35
>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 = 42.9 bits (100), Expect = 1e-04
Identities = 44/290 (15%), Positives = 95/290 (32%), Gaps = 95/290 (32%)
Query: 9 EIQKLAKEFLS-DPIQLNVGSANLAANPN------------IKQFVEICHEYEKPAKWWD 55
Q L +E L+ +P +L++ + ++ + +E +P
Sbjct: 314 RPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP----A 369
Query: 56 SNNGHY------PKSVRF---VLG----------TAGFLLSAVSFSLPFRDDKTSVVTVP 96
+ P S +L + +SL + K S +++P
Sbjct: 370 EYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIP 429
Query: 97 SYPDPSVNHLQGKTKEEIDSFRKEHNITLIGQ-NIPKPVKTLDETNIP--SYI---LGPM 150
+ + K ++++ H +++ NIPK + D Y +G
Sbjct: 430 --------SIYLELKVKLENEYALHR-SIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG-- 478
Query: 151 KPKTTNNENNHNKNKKCGDKESKNWTIPLNFQAKKFISVLQK-KAEVQSRSVFTYILPAL 209
+H KN + ++ + + L+F +F+ QK + + + + IL L
Sbjct: 479 ---------HHLKNIEHPERMTLFRMVFLDF---RFLE--QKIRHDSTAWNASGSILNTL 524
Query: 210 -----Y--HILK---------------MPKLEEGDGPIALVLAPTRELAQ 237
Y +I +PK+EE L+ + +L +
Sbjct: 525 QQLKFYKPYICDNDPKYERLVNAILDFLPKIEE-----NLICSKYTDLLR 569
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 40.4 bits (94), Expect = 7e-04
Identities = 22/123 (17%), Positives = 34/123 (27%), Gaps = 44/123 (35%)
Query: 175 WTIP--LNFQAKKFISVLQKKAEVQSRSVFTYILPALYHILKMPKLEEGDGPIALVLAPT 232
+P F A S LQ++ F ILP PT
Sbjct: 20 LLVPTASFFIA----SQLQEQ--------FNKILPE----------------------PT 45
Query: 233 RELAQ--QIQAVISIFSRTMR-IRHACLYGGTSKMYQVILLRILTSATNTSLGIYLQQND 289
A + + + + + + +L LT N YL+ ND
Sbjct: 46 EGFAADDEPTTPAELVGKFLGYVSSLVE-PSKVGQFDQVLNLCLTEFENC----YLEGND 100
Query: 290 AHS 292
H+
Sbjct: 101 IHA 103
Score = 30.0 bits (67), Expect = 1.2
Identities = 26/151 (17%), Positives = 50/151 (33%), Gaps = 48/151 (31%)
Query: 59 GHYPKSVRFVLG--TAGFLLSAVSFSLPFRDDKTSVVTVPSYPDPSVNHLQGKTKEEIDS 116
GH S LG A L++++ + + VV +G T +
Sbjct: 1761 GH---S----LGEYAA---LASLADVMSI-ESLVEVV-----------FYRGMTMQVAVP 1798
Query: 117 FRKEH---NITLIGQNIPKPVKTLDETNIPSYILGPMKPKTTNNEN----NHNKNKKC-- 167
R E N +I N + + + + Y++ + +T N+N
Sbjct: 1799 -RDELGRSNYGMIAINPGRVAASFSQEAL-QYVVERVGKRT--GWLVEIVNYN----VEN 1850
Query: 168 ------GDKESKNWTIP-LNFQAKKFISVLQ 191
GD + + LNF + I +++
Sbjct: 1851 QQYVAAGDLRALDTVTNVLNFIKLQKIDIIE 1881
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 33.9 bits (77), Expect = 0.038
Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 9/59 (15%)
Query: 142 IPSY--ILGPMKPKTTNNENNHNKNKKCG--DKESKNWTIPLNFQAKKFISVLQKKAEV 196
+P + NN+ NKKC D SK + + F+ + Q++A+V
Sbjct: 178 LPPNEILFSENNDMDNNNDGVDELNKKCTFWDAISKLYYVQFFFKQAE-----QEQADV 231
>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 = 32.3 bits (73), Expect = 0.24
Identities = 15/88 (17%), Positives = 23/88 (26%), Gaps = 18/88 (20%)
Query: 214 KMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLRIL 273
K+P G LVL P+ A + A + V R +
Sbjct: 248 KVPAAYAAQGYKVLVLNPSVAATLGFGA---------YMSKA-HGIDPNIRTGV---RTI 294
Query: 274 TSATN----TSLGIYLQQNDAHSPCLSV 297
T+ T G +L +
Sbjct: 295 TTGAPVTYSTY-GKFLADGGCSGGAYDI 321
>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein;
HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19
c.37.1.19 PDB: 2fzl_A*
Length = 472
Score = 31.0 bits (70), Expect = 0.49
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSKMYQVILLRILTSATN 278
L++ PT LA+Q + + IF + + G K + + + SA
Sbjct: 136 TLIVVPTLALAEQWKERLGIFG----EEYVGEFSGRIKELKPLTVSTYDSAYV 184
>3ne5_A Cation efflux system protein CUSA; transmembrane helix, metal
transport; 2.90A {Escherichia coli} PDB: 3k07_A 3k0i_A
3kso_A 3kss_A
Length = 1054
Score = 30.2 bits (69), Expect = 1.1
Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 13/48 (27%)
Query: 215 MPKLEEGDGPIALVLAP------TRELAQQIQAVI-------SIFSRT 249
+P++ EGD P + Q+ +I +F +T
Sbjct: 569 LPQINEGDLLYMPSTLPGISAAEAASMLQKTDKLIMSVPEVARVFGKT 616
>3u1s_H FAB PGT145 heavy chain; IGG, broadly neutralizing antibody, HIV-1
GP120, immune SYST; HET: TYS; 2.30A {Homo sapiens}
Length = 267
Score = 29.4 bits (67), Expect = 1.4
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 90 TSVVTVPSYPDPS------VNHLQGKTK 111
+SVVTVPS + VNH TK
Sbjct: 229 SSVVTVPSSSLGTQTYICNVNHKPSNTK 256
>3liz_H 4C3 monoclonal antibody heavy chain; hydrolase-immune system
complex; HET: NAG BMA MAN; 1.80A {Mus musculus} PDB:
3rvv_D* 3rvu_D 3rvt_D* 3rvw_D* 3rvx_D 1lo4_H 1ub6_H
3r06_B 3r08_H
Length = 253
Score = 28.3 bits (64), Expect = 3.1
Identities = 17/72 (23%), Positives = 25/72 (34%), Gaps = 15/72 (20%)
Query: 90 TSVVTVPSYPDPS------VNHLQGKTKEEIDSFRKEHNITLIGQNIPKPVKTLDETNIP 143
+S VTVPS PS V H TK + ++ ++ +
Sbjct: 184 SSSVTVPSSTWPSETVTCNVAHPASSTKV---------DKKIVPRDCGCKPCICTVPEVS 234
Query: 144 SYILGPMKPKTT 155
S + P KPK
Sbjct: 235 SVFIFPPKPKDV 246
>2okj_A Glutamate decarboxylase 1; PLP-dependent decarboxylase, lyase; HET:
LLP PLZ; 2.30A {Homo sapiens} PDB: 2okk_A*
Length = 504
Score = 28.5 bits (64), Expect = 3.8
Identities = 23/128 (17%), Positives = 44/128 (34%), Gaps = 19/128 (14%)
Query: 192 KKAEVQSRSVFTYILPA-LYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTM 250
+K +S V + P L ++ LE D P ++ + + RT
Sbjct: 37 RKTFDRSTKVLDFHHPHQLLEGMEGFNLELSDHP-----ESLEQILVDCRDTLKYGVRTG 91
Query: 251 RIR-HACLYGGTSKMYQVILLRILTSATNTSLGIYLQQNDAHSPCLS-----VWRRLQDI 304
R L G + LTS NT++ Y +P +++++I
Sbjct: 92 HPRFFNQLSTGLD--IIGLAGEWLTSTANTNMFTY-----EIAPVFVLMEQITLKKMREI 144
Query: 305 LGLTEETC 312
+G + +
Sbjct: 145 VGWSSKDG 152
>2jg0_A Periplasmic trehalase; family 37, hydrolase, inhibitor, glycoside
hydrolase, glycosidase, 1-thiatrehazolin; HET: TTZ;
1.50A {Escherichia coli} SCOP: a.102.1.9 PDB: 2jf4_A*
2jjb_A* 2wyn_A*
Length = 535
Score = 28.3 bits (62), Expect = 3.8
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 4/53 (7%)
Query: 73 GFLLSAVSFSLPFRDDKTSVVTVPSYPDPSV----NHLQGKTKEEIDSFRKEH 121
G L + V + F D KT VP+ + Q ++ ++ F +
Sbjct: 15 GPLFNDVQNAKLFPDQKTFADAVPNSDPLMILADYRMQQNQSGFDLRHFVNVN 67
>3n9g_H FAB fragment of MAB CR4354, heavy chain; human neutralizing
antibody, immun anti-WEST NIle virus; 1.43A {Homo
sapiens} PDB: 3iyw_H 3qeh_A 3u0t_D 3c08_H 3lmj_H 3lqa_H*
3c09_H* 3pp4_H 3pp3_H 2jb5_H* 2jb6_B* 2eh7_H 2eh8_H
3jwd_H* 3jwo_H* 3t2n_H 3qot_H 3ma9_H 3nfs_H 3nfp_A ...
Length = 230
Score = 27.4 bits (62), Expect = 4.9
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 90 TSVVTVPSYPDPS------VNHLQGKTK 111
+SVVTVPS + VNH TK
Sbjct: 189 SSVVTVPSSSLGTQTYICNVNHKPSNTK 216
>2jis_A Cysteine sulfinic acid decarboxylase; pyridoxal phosphate,
alternative splicing, pyridoxal phosphate (PLP),
structural genomics consortium (SGC); HET: PLP; 1.6A
{Homo sapiens}
Length = 515
Score = 27.7 bits (62), Expect = 5.0
Identities = 29/175 (16%), Positives = 62/175 (35%), Gaps = 34/175 (19%)
Query: 151 KPKTTNNENNHNKNKKCGDKESKNWTIPLNFQA------KKFISVLQKKAEVQSRSVFTY 204
EN + ++ + P+ +A + +K S+ V +
Sbjct: 9 SGVDLGTENLYFQSMADSEALPSLAGDPVAVEALLRAVFGVVVDEAIQKGTSVSQKVCEW 68
Query: 205 ILPA-LYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRH----ACLYG 259
P L +L + +G+ +++ ++ +AVI +++ H L+
Sbjct: 69 KEPEELKQLLDLELRSQGE--------SQKQILERCRAVIR---YSVKTGHPRFFNQLFS 117
Query: 260 GTSKMYQVILLRILTSATNTSLGIYLQQNDAHSPCLS-----VWRRLQDILGLTE 309
G + RI+T + NTS Y +P V R+L+ ++G +
Sbjct: 118 GLD--PHALAGRIITESLNTSQYTY-----EIAPVFVLMEEEVLRKLRALVGWSS 165
>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 = 27.8 bits (61), Expect = 5.2
Identities = 10/38 (26%), Positives = 13/38 (34%)
Query: 226 ALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTSK 263
L+LAPT+ L Q + L G S
Sbjct: 55 VLMLAPTKPLVLQHAESFRRLFNLPPEKIVALTGEKSP 92
>3tv3_H PGT128 heavy chain, IG gamma-1 chain C region; FAB, HIV-1
neutralizing antibody, GP120, immune system; HET: PCA
MAN GOL EPE; 1.29A {Homo sapiens} PDB: 3tyg_H* 3twc_H*
3tje_H* 3thm_H* 2xzc_H* 2xza_H* 3b2u_H* 3b2v_H* 3mly_H
3mlz_H 2ykl_H* 2yk1_H* 3mlx_H 2jix_D 2vxq_H 3hi1_H*
3uc0_H 3uaj_H 3q1s_H 3fn0_H ...
Length = 239
Score = 27.5 bits (62), Expect = 5.7
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 90 TSVVTVPSYPDPS------VNHLQGKTK 111
+SVVTVPS + VNH TK
Sbjct: 201 SSVVTVPSSSLGTQTYICNVNHKPSNTK 228
>1f6y_A 5-methyltetrahydrofolate corrinoid/iron sulfur PR
methyltransferase; carbon dioxide fixation, cobalamin,
methyltatrahydrofolate; 2.20A {Moorella thermoacetica}
SCOP: c.1.21.2 PDB: 2e7f_A* 4djd_A* 4dje_A* 4djf_A*
2ogy_A*
Length = 262
Score = 27.5 bits (62), Expect = 5.7
Identities = 15/67 (22%), Positives = 22/67 (32%), Gaps = 19/67 (28%)
Query: 20 DPIQLNVGSANLAANPNIKQFVEICHEYEKPAKWWDSNNGHYPKSVRFVLGTAGFLLSAV 79
DP+ L A A + + ++ PA + VLG LS V
Sbjct: 160 DPLILPANVAQDHAP-EVLKTLQQIKMLADPA-------------PKTVLG-----LSNV 200
Query: 80 SFSLPFR 86
S + R
Sbjct: 201 SQNCQNR 207
>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H
RNA-binding helicase, innate immunity, IFIH1, S
genomics; 1.60A {Homo sapiens}
Length = 216
Score = 27.5 bits (61), Expect = 5.8
Identities = 8/44 (18%), Positives = 12/44 (27%), Gaps = 2/44 (4%)
Query: 208 ALYHILKMPKLEEGDGPIALVLAPTRELA-QQIQAVISIFSRTM 250
L K G + +VL L Q + F +
Sbjct: 68 IAKDHLDKKKKASEPGKV-IVLVNKVLLVEQLFRKEFQPFLKKW 110
>3mlr_H Human monoclonal anti-HIV-1 GP120 V3 antibody 255 heavy chain;
human monoclonal antibody, FAB, third variable
antibody-antigen interaction; 1.80A {Homo sapiens} PDB:
3mls_H 3mlt_H 3mlu_H 3mlv_H
Length = 226
Score = 27.4 bits (62), Expect = 6.1
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 90 TSVVTVPSYPDPS------VNHLQGKTK 111
+SVVTVPS + VNH TK
Sbjct: 190 SSVVTVPSSSLGTQTYICNVNHKPSNTK 217
>3u2s_H PG9 heavy chain; greek KEY, immunoglobulin, immune recognition,
immune system; HET: PCA TYS BU3 NAG BMA MAN; 1.80A {Homo
sapiens} PDB: 3u4e_H* 3u36_H 3mug_B* 3lrs_H* 3mme_H*
2qsc_H*
Length = 248
Score = 27.1 bits (61), Expect = 6.4
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 90 TSVVTVPSYPDPS------VNHLQGKTK 111
+SVVTVPS + VNH TK
Sbjct: 202 SSVVTVPSSSLGTQTYICNVNHKPSNTK 229
>3sob_H Antibody heavy chain, low-density lipoprotein receptor-related
protein; beta propeller, protein binding-immune system
complex; 1.90A {Homo sapiens} PDB: 1pkq_B
Length = 256
Score = 27.1 bits (61), Expect = 6.9
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 90 TSVVTVPSYPDPS------VNHLQGKTK 111
+SVVTVPS + VNH TK
Sbjct: 215 SSVVTVPSSSLGTQTYICNVNHKPSNTK 242
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 27.6 bits (60), Expect = 7.0
Identities = 13/55 (23%), Positives = 19/55 (34%), Gaps = 2/55 (3%)
Query: 208 ALYHILKMPKLEEGDGPIALVLAPTRELAQQIQAVISIFSRTMRIRHACLYGGTS 262
H LK K G + A + +Q V S + + A + G TS
Sbjct: 39 ICEHHLK--KFPCGQKGKVVFFANQIPVYEQQATVFSRYFERLGYNIASISGATS 91
>1mju_H Immunoglobulin MS6-12; catalytic antibody, ester hydrolysis,
esterolytic, FAB, immune system; 1.22A {Mus musculus}
SCOP: b.1.1.1 b.1.1.2 PDB: 1mjj_B 1mie_H 1mj7_H* 1mj8_H
1mh5_B* 4aeh_H 2y5t_A 2vwe_E 2op4_H 2ntf_H 3loh_C 1e4x_H
2vl5_A 1e4x_I 1e4w_H 3opz_H 3oz9_H 1plg_H 1hi6_B 1cfn_B
...
Length = 227
Score = 27.1 bits (61), Expect = 7.2
Identities = 11/28 (39%), Positives = 12/28 (42%), Gaps = 6/28 (21%)
Query: 90 TSVVTVPSYPDPS------VNHLQGKTK 111
+S VTV S PS V H TK
Sbjct: 181 SSSVTVTSSTWPSQSITCNVAHPASSTK 208
>1c5d_H Monoclonal antibody against the main immunogenic the human muscle
acetylcholine receptor...; immunoglobulin, immune
system; 2.40A {Rattus norvegicus} SCOP: b.1.1.1 b.1.1.2
PDB: 2arj_H 3b9k_H* 2gk0_H 2gjz_H 1fn4_B 3mj8_H 3mj9_H*
Length = 215
Score = 27.1 bits (61), Expect = 7.3
Identities = 9/26 (34%), Positives = 12/26 (46%), Gaps = 4/26 (15%)
Query: 90 TSVVTVPSYPDPS----VNHLQGKTK 111
TS VT ++P + V H TK
Sbjct: 182 TSSVTSSTWPSQTVTCNVAHPASSTK 207
>1c1e_H Catalytic antibody 1E9 (heavy chain); diels-alder, immunoglobulin,
immune system; HET: ENH; 1.90A {Mus musculus} SCOP:
b.1.1.1 b.1.1.2 PDB: 1dbb_H* 1dba_H* 1dbj_H* 1dbk_H*
1dbm_H* 2dbl_H* 3ojd_B 1jgl_H* 1jhk_H 1ghf_H 1tet_H*
3e8u_H 1fj1_B 1cl7_H
Length = 219
Score = 26.7 bits (60), Expect = 9.9
Identities = 13/28 (46%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 90 TSVVTVPSYPDPS------VNHLQGKTK 111
+S VTVPS P PS V H TK
Sbjct: 184 SSSVTVPSSPRPSETVTCNVAHPASSTK 211
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 0.133 0.398
Gapped
Lambda K H
0.267 0.0470 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,615,597
Number of extensions: 257451
Number of successful extensions: 732
Number of sequences better than 10.0: 1
Number of HSP's gapped: 717
Number of HSP's successfully gapped: 104
Length of query: 317
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 223
Effective length of database: 4,077,219
Effective search space: 909219837
Effective search space used: 909219837
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: 57 (26.4 bits)