RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14604
(209 letters)
>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double
chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces
cerevisiae}
Length = 800
Score = 188 bits (480), Expect = 5e-56
Identities = 50/154 (32%), Positives = 75/154 (48%), Gaps = 6/154 (3%)
Query: 55 KTKTKELQEDEDGASGSKPRRYTPPPEKPTTDLRKKYEKQPPFLDDTGMQLHAYQLEGIN 114
+ K Q E+ + +K QPPF+ G +L +QL GIN
Sbjct: 193 PEQVKHFQNRENSKILPQYSSNYTSQRPR----FEKLSVQPPFI--KGGELRDFQLTGIN 246
Query: 115 WLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAPLSTIINWEREFE 174
W+ + W + + ILADEMGLGKT+QT+ F+ L GP ++ PLST+ W FE
Sbjct: 247 WMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPAWLDTFE 306
Query: 175 TWAPDFYVVTYVGDKDCRIVLRDHDISWEDTANR 208
WAPD + Y+G++ R +R+++ A
Sbjct: 307 KWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKG 340
>1z3i_X Similar to RAD54-like; recombination ATPase helicase,
recombination-DNA binding COM; 3.00A {Danio rerio} SCOP:
c.37.1.19 c.37.1.19
Length = 644
Score = 145 bits (367), Expect = 1e-40
Identities = 37/138 (26%), Positives = 55/138 (39%), Gaps = 13/138 (9%)
Query: 76 YTPPPEKPTTDLRKKYEKQPPFL---DDTGMQLHAYQLEGINWL-----RYSWGQNIDTI 127
Y PP ++ EK P + L +Q EG+ +L + I
Sbjct: 24 YEPPAISAHDLIKADKEKLPVHVVVDPVLSKVLRPHQREGVKFLWDCVTGRRIENSYGCI 83
Query: 128 LADEMGLGKTIQTITFLYSLFKEGHCKGP----FLVSAPLSTIINWEREFETWAPDF-YV 182
+ADEMGLGKT+Q IT +++L K+ P +V +P S + NW E W
Sbjct: 84 MADEMGLGKTLQCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQP 143
Query: 183 VTYVGDKDCRIVLRDHDI 200
V G I + +
Sbjct: 144 VAIDGGSKDEIDSKLVNF 161
>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex,
hydrolase/DNA complex complex; 3.00A {Sulfolobus
solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A
Length = 500
Score = 105 bits (265), Expect = 7e-27
Identities = 36/97 (37%), Positives = 50/97 (51%), Gaps = 2/97 (2%)
Query: 104 QLHAYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAPL 163
L YQ++G +W+R+ LAD+MGLGKT+QTI K+ + P LV PL
Sbjct: 37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVFSDA-KKENELTPSLVICPL 95
Query: 164 STIINWEREFETWAPDFYVVTYVGDKDCRIVLRDHDI 200
S + NWE E +AP + D+ L D+DI
Sbjct: 96 SVLKNWEEELSKFAPHLRFAVFHEDRSKIK-LEDYDI 131
>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 = 86.3 bits (213), Expect = 7e-20
Identities = 21/96 (21%), Positives = 35/96 (36%), Gaps = 4/96 (4%)
Query: 98 LDDTGMQLHAYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPF 157
L L +QL + + + +LADE+GLGKTI+ L+ G +
Sbjct: 147 LRGQRTSLIPHQLNIAHDVGRRHAPRV--LLADEVGLGKTIEAGMILHQQLLSGAAE-RV 203
Query: 158 LVSAPLSTIINWEREFETW-APDFYVVTYVGDKDCR 192
L+ P + W E F + + +
Sbjct: 204 LIIVPETLQHQWLVEMLRRFNLRFALFDDERYAEAQ 239
>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 = 38.0 bits (87), Expect = 0.001
Identities = 22/153 (14%), Positives = 45/153 (29%), Gaps = 11/153 (7%)
Query: 16 KKKKKSTGRASKAADDDDDEDLKAAYFNDGKKKKSKGRGKTKTKELQEDEDGASGSKPRR 75
+ K+ ++ + A D + + ++ + ++ + ED AS +
Sbjct: 162 RSDKEHWPKSLQLALDTTGYYRASELW--DIREDNAKDVDSEMTDASEDCLEASMTYSEE 219
Query: 76 YTPPPEKPTTDLRKKYEKQPPFLDDTGMQLHAYQLEGINWLRYSWGQNIDTILADEMGLG 135
P P + +YQ+E + ++ G G
Sbjct: 220 AEPDDNLSENLGSAAEGIGKPPPVYETKKARSYQIELAQPAI----NGKNALICAPTGSG 275
Query: 136 KTIQTITFLYSLFK----EGHCKGPFLV-SAPL 163
KT +I F+ K FL P+
Sbjct: 276 KTFVSILICEHHFQNMPAGRKAKVVFLATKVPV 308
>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 = 37.5 bits (86), Expect = 0.002
Identities = 31/203 (15%), Positives = 62/203 (30%), Gaps = 46/203 (22%)
Query: 17 KKKKSTGRASKAADDDDDEDLKAAYFNDGKKKKSKGR-GKTKTKELQEDEDGASGSKPRR 75
K+++ + + + + L + K + + T+ Q D +
Sbjct: 74 KQEEMVQKFVEEVLRINYKFLMSPI-----KTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128
Query: 76 YTPPPEKPTTDLRKK-YEKQP-PFLDDTGMQ-----------LHAYQLE-----GINWLR 117
Y +P LR+ E +P + G+ +Y+++ I WL
Sbjct: 129 YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN 188
Query: 118 YSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAP---LSTIINWEREFE 174
+ +T+L EM +Q L S + +I R
Sbjct: 189 LKNCNSPETVL--EM-----LQK---LLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238
Query: 175 TWAPDFYVVTYVGDKDCRIVLRD 197
P Y ++C +VL +
Sbjct: 239 KSKP------Y---ENCLLVLLN 252
>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 = 35.2 bits (80), Expect = 0.012
Identities = 17/90 (18%), Positives = 29/90 (32%), Gaps = 10/90 (11%)
Query: 103 MQLHAYQLEGINWLRYSWGQNIDTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLV-SA 161
+Q YQ + + + ++ GLGKT+ + + K L +
Sbjct: 8 IQPRIYQEVIYAKCKET-----NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTK 62
Query: 162 PLSTIINWEREFETWA--PDFYVVTYVGDK 189
PL F P +V G+K
Sbjct: 63 PLVLQ--HAESFRRLFNLPPEKIVALTGEK 90
>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 = 33.5 bits (76), Expect = 0.056
Identities = 33/221 (14%), Positives = 64/221 (28%), Gaps = 69/221 (31%)
Query: 25 ASKAADDDDDEDLKA-----AYFNDGKKKKSKGRGKTKTKE---LQEDEDGASGSKPRRY 76
A+K ++D +K Y + R K + +G + +
Sbjct: 105 AAKLLQENDTTLVKTKELIKNYI---TARIMAKRPFDKKSNSALFRAVGEGNA----QLV 157
Query: 77 TP-----PPEKPTTDLRKKYEKQPPFLDDTGMQLHAYQLE---------------GINWL 116
+ +LR Y+ + D ++ A L G+N L
Sbjct: 158 AIFGGQGNTDDYFEELRDLYQTYHVLVGDL-IKFSAETLSELIRTTLDAEKVFTQGLNIL 216
Query: 117 RYSWGQNIDTILADE-----------MGLGKTIQTITFLYSL------FKE------GHC 153
W +N + +G+ + + L + GH
Sbjct: 217 --EWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHS 274
Query: 154 KGPFLVSA-PLSTIINWEREFETWAPDFY-VVTYVGDKDCR 192
+G LV+A ++ +WE F V+ ++G R
Sbjct: 275 QG--LVTAVAIAETDSWE-SFFVSVRKAITVLFFIG---VR 309
Score = 26.9 bits (59), Expect = 5.9
Identities = 20/130 (15%), Positives = 40/130 (30%), Gaps = 42/130 (32%)
Query: 74 RRYTPPPEKPTTDLRKKY-EKQP-----------PF----LDD-TGMQLHAYQLEGINWL 116
R+ P + R + E++ PF L + + +++
Sbjct: 394 RKAKAPSGLDQS--RIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFN 451
Query: 117 RYSWGQNI---DTILADEMGLGKTIQTITFLYSLFKEGHCKGPFLVSAPLSTIINWER-- 171
I DT D G ++ ++ S+ +V + + WE
Sbjct: 452 AKDIQ--IPVYDT--FD----GSDLRVLS--GSI-------SERIVDCIIRLPVKWETTT 494
Query: 172 EFE-TWAPDF 180
+F+ T DF
Sbjct: 495 QFKATHILDF 504
Score = 26.9 bits (59), Expect = 6.9
Identities = 7/18 (38%), Positives = 8/18 (44%)
Query: 53 RGKTKTKELQEDEDGASG 70
RG T + DE G S
Sbjct: 1789 RGMTMQVAVPRDELGRSN 1806
>3h1t_A Type I site-specific restriction-modification system, R
(restriction) subunit; hydrolase, restriction enzyme
HSDR, ATP-binding; 2.30A {Vibrio vulnificus}
Length = 590
Score = 32.8 bits (75), Expect = 0.075
Identities = 15/63 (23%), Positives = 21/63 (33%), Gaps = 3/63 (4%)
Query: 96 PFLDDTGMQLHAYQLEGINWLRYSWGQNIDTILADEM--GLGKTIQTITFLYSLFKEGHC 153
P+ +G YQ IN S Q L M G GKT+ + L+
Sbjct: 170 PYHHVSGYSPRYYQQIAINRAVQSVLQGKKRSLI-TMATGTGKTVVAFQISWKLWSARWN 228
Query: 154 KGP 156
+
Sbjct: 229 RTG 231
>1q0v_A Hydrophilic protein; has cysteine rich putative zinc finger
esential for function;...; stable, non-interacting
alpha-helices; NMR {Saccharomyces cerevisiae} SCOP:
j.105.1.1 PDB: 1q0w_A
Length = 81
Score = 28.2 bits (63), Expect = 0.47
Identities = 6/22 (27%), Positives = 12/22 (54%)
Query: 19 KKSTGRASKAADDDDDEDLKAA 40
+ + ++++D DLKAA
Sbjct: 40 ESKNEVKRQEIEEEEDPDLKAA 61
>2p4f_A Similar to SP|P32453 saccharomyces cerevisiae YNL ATP11; half
barrel, chaperone; HET: P6G; 1.40A {Candida glabrata
cbs 138}
Length = 299
Score = 28.9 bits (64), Expect = 1.2
Identities = 10/66 (15%), Positives = 22/66 (33%)
Query: 32 DDDEDLKAAYFNDGKKKKSKGRGKTKTKELQEDEDGASGSKPRRYTPPPEKPTTDLRKKY 91
+ E+LK + ++KK + +EL++ + S + + K
Sbjct: 31 ESIEELKKRLADQIEEKKKELNKIDPLRELEQHLNAGSRIHTNKEHKTTKMSNKSNEKSG 90
Query: 92 EKQPPF 97
P
Sbjct: 91 NVLPKD 96
>2fvy_A D-galactose-binding periplasmic protein; periplasmic binding
protien, hinge, chemotaxis, transport,; HET: BGC; 0.92A
{Escherichia coli} SCOP: c.93.1.1 PDB: 1glg_A* 2fw0_A*
2gbp_A* 2qw1_A* 2hph_A* 2ipn_A* 2ipm_A* 2ipl_A* 1gca_A*
1gcg_A 3ga5_A* 3gbp_A*
Length = 309
Score = 28.5 bits (64), Expect = 1.5
Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 16/71 (22%)
Query: 79 PPEKPTTDLRKKYEKQPPFLDDTGMQLHAYQLEGINWLR------------YSWGQNIDT 126
P P + R Y + L+D G++ QL+ W I+
Sbjct: 149 EPGHPDAEARTTYVIKE--LNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEV 206
Query: 127 ILA--DEMGLG 135
++A D M +G
Sbjct: 207 VIANNDAMAMG 217
>3cai_A Possible aminotransferase; RV3778C; 1.80A {Mycobacterium
tuberculosis}
Length = 406
Score = 28.0 bits (63), Expect = 2.6
Identities = 1/25 (4%), Positives = 7/25 (28%), Gaps = 3/25 (12%)
Query: 111 EGINWLRYSWGQNI---DTILADEM 132
++ L + ++ +
Sbjct: 97 VLLSLLAEASSSRAGLGYEVIVSRL 121
>2e7j_A SEP-tRNA:Cys-tRNA synthase; seven-stranded BETE-strand, lyase,
structural genomics; HET: PLP; 2.40A {Archaeoglobus
fulgidus} SCOP: c.67.1.9 PDB: 2e7i_A*
Length = 371
Score = 27.8 bits (62), Expect = 2.9
Identities = 4/22 (18%), Positives = 9/22 (40%)
Query: 111 EGINWLRYSWGQNIDTILADEM 132
E + +S + ++ DE
Sbjct: 80 EAKFAVMHSLAKKDAWVVMDEN 101
>1w2w_B 5-methylthioribose-1-phosphate isomerase; EIF2B, methionine salvage
pathway, translation initiation, oxidoreductase; 1.75A
{Saccharomyces cerevisiae} SCOP: c.124.1.5
Length = 191
Score = 26.4 bits (59), Expect = 5.4
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 156 PFLVSAPLSTI 166
F V AP +TI
Sbjct: 87 KFFVVAPKTTI 97
>1t3i_A Probable cysteine desulfurase; PLP-binding enzyme, transferase;
HET: 2OS PLP; 1.80A {Synechocystis SP} SCOP: c.67.1.3
Length = 420
Score = 26.7 bits (60), Expect = 5.4
Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 4/26 (15%)
Query: 111 EGINWLRYSWGQNI----DTILADEM 132
E IN + YSWG N D I+ M
Sbjct: 101 EAINLVAYSWGMNNLKAGDEIITTVM 126
>1kmj_A Selenocysteine lyase; persulfide perselenide NIFS pyridoxal
phosphate, structural PSI, protein structure initiative;
HET: PLP; 2.00A {Escherichia coli} SCOP: c.67.1.3 PDB:
1i29_A* 1jf9_A* 1kmk_A* 1c0n_A*
Length = 406
Score = 26.7 bits (60), Expect = 5.7
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 111 EGINWLRYSWGQNI----DTILADEM 132
EGIN + SWG + D I+ +M
Sbjct: 96 EGINLVANSWGNSNVRAGDNIIISQM 121
>2a0u_A Initiation factor 2B; SGPP, structural genomics, PSI, protein
structure initiative eukaryotic initiation factor; 2.10A
{Leishmania major} SCOP: c.124.1.5
Length = 383
Score = 26.8 bits (60), Expect = 5.9
Identities = 4/11 (36%), Positives = 7/11 (63%)
Query: 156 PFLVSAPLSTI 166
V+AP +T+
Sbjct: 292 KLYVAAPTTTL 302
>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A
{Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A*
1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A*
1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A*
2ga2_A* 2oaz_A*
Length = 478
Score = 26.8 bits (59), Expect = 6.3
Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 4/86 (4%)
Query: 11 AAARGKKKKKSTGRASKAADDDDDEDLKAAYFNDGKKKKSKGRGKTKTKELQEDEDGASG 70
A + +KKKKS G ++ + D E + + + R + KE ED++ G
Sbjct: 35 AKKKRRKKKKSKGPSAAGEQEPDKESGASV----DEVARQLERSALEDKERDEDDEDGDG 90
Query: 71 SKPRRYTPPPEKPTTDLRKKYEKQPP 96
+K K + PP
Sbjct: 91 DGDGATGKKKKKKKKKRGPKVQTDPP 116
>1t5o_A EIF2BD, translation initiation factor EIF2B, subunit DELT; subunit
delta, structural GEN PSI, protein structure initiative;
1.90A {Archaeoglobus fulgidus} SCOP: c.124.1.5
Length = 351
Score = 26.1 bits (58), Expect = 9.0
Identities = 6/11 (54%), Positives = 8/11 (72%)
Query: 156 PFLVSAPLSTI 166
PF V+AP +T
Sbjct: 260 PFYVAAPKATF 270
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
0.314 0.134 0.408
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,373,996
Number of extensions: 196438
Number of successful extensions: 377
Number of sequences better than 10.0: 1
Number of HSP's gapped: 371
Number of HSP's successfully gapped: 36
Length of query: 209
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 120
Effective length of database: 4,216,824
Effective search space: 506018880
Effective search space used: 506018880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (24.8 bits)