RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13032
(190 letters)
>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double
chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces
cerevisiae}
Length = 800
Score = 151 bits (384), Expect = 4e-43
Identities = 40/143 (27%), Positives = 75/143 (52%), Gaps = 15/143 (10%)
Query: 2 ERFVPDFKVVPYWGSPQERKILRQ---FWDMKNLHTKDASFHVVITSYQLVVSDFKYFNR 58
E++ PD + Y G+ + R +R+ + + + K F+V++T+Y+ ++ D
Sbjct: 306 EKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAELGS 365
Query: 59 IKWQYLILDEAQAIVDINVYSYLNDIEREQSMRWKLLLGFSCRNRLLLSGTPIQNSMAEL 118
IKWQ++ +DEA + + +S ++ L F NR+L++GTP+QN++ EL
Sbjct: 366 IKWQFMAVDEAHRL------------KNAESSLYESLNSFKVANRMLITGTPLQNNIKEL 413
Query: 119 WALLHFIMPSMFDSHDEFNEWFS 141
AL++F+MP F E +
Sbjct: 414 AALVNFLMPGRFTIDQEIDFENQ 436
>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 = 123 bits (310), Expect = 4e-33
Identities = 30/161 (18%), Positives = 62/161 (38%), Gaps = 20/161 (12%)
Query: 2 ERFVPDF-KVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDFKYFNRIK 60
+++ + V G ++ + + + ++I SY+ + ++ K
Sbjct: 134 GKWLGGRVQPVAIDGGSKDEID-SKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGK 192
Query: 61 WQYLILDEAQAIVDINVYSYLNDIER---EQSMRWKLLLGFSCRNRLLLSGTPIQNSMAE 117
+I DE R + + L + + R+L+SGTPIQN + E
Sbjct: 193 VGLVICDEGH---------------RLKNSDNQTYLALNSMNAQRRVLISGTPIQNDLLE 237
Query: 118 LWALLHFIMPSMFDSHDEFNEWFSKDIESHAENKTSIDERE 158
++L+HF+ + + EF + F I + S +R
Sbjct: 238 YFSLVHFVNSGILGTAQEFKKRFEIPILKGRDADASDKDRA 278
>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 = 114 bits (287), Expect = 3e-30
Identities = 32/150 (21%), Positives = 69/150 (46%), Gaps = 27/150 (18%)
Query: 2 ERFVPDFKVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDFKYFNRIKW 61
+F P + + + K+ + +++T+Y +++ D + ++W
Sbjct: 106 SKFAPHLRFAVFHEDRSKIKL--------------EDYDIILTTYAVLLRDTRL-KEVEW 150
Query: 62 QYLILDEAQAIVDINVYSYLNDIEREQSMRWKLLLGFSCRNRLLLSGTPIQNSMAELWAL 121
+Y+++DEAQ I N Q+ +K + + R+ L+GTPI+N + +LW++
Sbjct: 151 KYIVIDEAQNIK--NP----------QTKIFKAVKELKSKYRIALTGTPIENKVDDLWSI 198
Query: 122 LHFIMPSMFDSHDEFNEWFSKDIESHAENK 151
+ F+ P + S+ EF F+ I+
Sbjct: 199 MTFLNPGLLGSYSEFKSKFATPIKKGDNMA 228
>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 = 85.9 bits (212), Expect = 6e-20
Identities = 29/149 (19%), Positives = 48/149 (32%), Gaps = 23/149 (15%)
Query: 2 ERFVPDFKVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSD---FKYFNR 58
RF F + + + +D + +VI S ++
Sbjct: 221 RRFNLRFALFDDERYAEAQHDAYNPFD---------TEQLVICSLDFARRSKQRLEHLCE 271
Query: 59 IKWQYLILDEAQAIVDINVYSYLNDIEREQSMRWKLL--LGFSCRNRLLLSGTPIQNSMA 116
+W L++DEA L E S ++ + L LLL+ TP Q M
Sbjct: 272 AEWDLLVVDEAHH---------LVWSEDAPSREYQAIEQLAEHVPGVLLLTATPEQLGME 322
Query: 117 ELWALLHFIMPSMFDSHDEFNEWFSKDIE 145
+A L + P+ F +F E
Sbjct: 323 SHFARLRLLDPNRFHDFAQFVEEQKNYCP 351
>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 = 41.6 bits (97), Expect = 8e-05
Identities = 17/94 (18%), Positives = 31/94 (32%), Gaps = 21/94 (22%)
Query: 114 SMAELWA-LLHFIM-------PSMFD-----SHDEFNEWF--SKDIESHAENKTSIDERE 158
+ AEL L ++ FD EF + DI + A ++
Sbjct: 56 TPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTT 115
Query: 159 YPIVLMLI---YSAHNKAEKSLYSSSRRASSPLL 189
LI +A A++ ++++S L
Sbjct: 116 LVKTKELIKNYITARIMAKRPF---DKKSNSALF 146
>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 = 34.8 bits (79), Expect = 0.013
Identities = 24/144 (16%), Positives = 51/144 (35%), Gaps = 24/144 (16%)
Query: 22 ILRQFWDMKNLHTKDASFHVVITSYQLVVSDFKYFNRIKWQYLILDEAQAIVDINVYSYL 81
+L + K + + S +++T+ V+DF ++ LD
Sbjct: 249 VLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTT--HISLDHHS----------- 295
Query: 82 NDIEREQSMRWKLLLGF-SCRNRLL----LSGTPIQNSMAELWALLHFIMPSMFDSHDEF 136
+ ++ LLL + CR + L L+ P + S+ + + + +D+
Sbjct: 296 MTLTPDEVK--SLLLKYLDCRPQDLPREVLTTNPRRLSI--IAESIR-DGLATWDNWKHV 350
Query: 137 NEW-FSKDIESHAENKTSIDEREY 159
N + IES + R+
Sbjct: 351 NCDKLTTIIESSLNVLEPAEYRKM 374
Score = 29.4 bits (65), Expect = 0.87
Identities = 25/189 (13%), Positives = 57/189 (30%), Gaps = 43/189 (22%)
Query: 2 ERFVPDFKVVPY---WGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDFKYFNR 58
++FV + + Y + + + +D ++ + VS + + +
Sbjct: 80 QKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLK 139
Query: 59 IKWQYLILDEAQAIVDINVY------------SYLNDIEREQSMR----WKLLLGFSCRN 102
++ L L A+ ++ + + + M W L L
Sbjct: 140 LRQALLELRPAKNVL---IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW-LNLKNCNSP 195
Query: 103 RLLLSGTPIQNSMAELWALLHFIMPSMFDSHDEFNEWFSKDIESHAEN-----KTSIDER 157
+L L LL+ I P+ D S +I+ + + + +
Sbjct: 196 ETVL---------EMLQKLLYQIDPNWTSRSD-----HSSNIKLRIHSIQAELRRLLKSK 241
Query: 158 EYPIVLMLI 166
Y L L+
Sbjct: 242 PYENCL-LV 249
>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling,
archaea, isomeras; 2.35A {Thermotoga maritima} PDB:
3p4y_A 3p4x_A*
Length = 414
Score = 31.2 bits (71), Expect = 0.17
Identities = 16/104 (15%), Positives = 40/104 (38%), Gaps = 16/104 (15%)
Query: 7 DFKVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDFKYFNRIKWQYLIL 66
K+ ++ S K + K+ D +H+++ S Q V + + ++ ++ ++ +
Sbjct: 91 KVKIFGFYSS---MKKEEKEKFEKSFEEDD--YHILVFSTQFVSKNREKLSQKRFDFVFV 145
Query: 67 DEAQAIVDINVYSYLNDIEREQSMRWKLLLGFS-CRNRLLLSGT 109
D+ A++ S D +++G R S
Sbjct: 146 DDVDAVLKA---SRNIDTLL-------MMVGIPEEIIRKAFSTI 179
>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 = 30.9 bits (69), Expect = 0.25
Identities = 24/146 (16%), Positives = 46/146 (31%), Gaps = 27/146 (18%)
Query: 6 PDFKVVPYWG--SPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSDF--KYFNRIKW 61
P K+V G SP+ER + W V++ + Q + +D +
Sbjct: 79 PPEKIVALTGEKSPEERS---KAWA---------RAKVIVATPQTIENDLLAGRISLEDV 126
Query: 62 QYLILDEAQAIVDINVYSYLNDIEREQSMRWKLLLGFSCRNRLLLSGTPI--QNSMAELW 119
++ DEA V Y ++ + Q+ + L+ +P + E+
Sbjct: 127 SLIVFDEAHRAVGNYAYVFIAREYKRQA---------KNPLVIGLTASPGSTPEKIMEVI 177
Query: 120 ALLHFIMPSMFDSHDEFNEWFSKDIE 145
L + + K I
Sbjct: 178 NNLGIEHIEYRSENSPDVRPYVKGIR 203
>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 = 28.6 bits (64), Expect = 1.4
Identities = 12/95 (12%), Positives = 29/95 (30%), Gaps = 16/95 (16%)
Query: 41 VVITSYQLVVSDFKYFNRIKWQYLILDEAQAIVDINVYSYLNDIEREQSMRWKLLLGFSC 100
+ +++Y + + ++ LI DE + Y ++
Sbjct: 174 LTVSTYDSAYVNAEKLGN-RFMLLIFDEVHHLPA-ESYV-------------QIAQMSIA 218
Query: 101 RNRLLLSGTPIQNSMAELWALLHFIMPSMFDSHDE 135
RL L+ T + L + +F+ +
Sbjct: 219 PFRLGLTATFEREDGRH-EILKEVVGGKVFELFPD 252
>1tp6_A Hypothetical protein PA1314; structural genomics, alpha-beta
sandwich, PSI, protein structure initiative; 1.50A
{Pseudomonas aeruginosa PAO1} SCOP: d.17.4.12
Length = 128
Score = 26.1 bits (57), Expect = 4.8
Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 2/52 (3%)
Query: 1 MERFVPDFKVVPYWGSPQERKILRQFWDMKNLHTKDASFHVVITSYQLVVSD 52
M RF DF +V G ++ L + ++ + I L+ S
Sbjct: 33 MARFAEDFSMVTPHGVVLDKTALGEL--FRSKGGTRPGLRIEIDGESLLASG 82
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
0.322 0.135 0.415
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,947,443
Number of extensions: 161787
Number of successful extensions: 323
Number of sequences better than 10.0: 1
Number of HSP's gapped: 314
Number of HSP's successfully gapped: 18
Length of query: 190
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 102
Effective length of database: 4,244,745
Effective search space: 432963990
Effective search space used: 432963990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.7 bits)