RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2046
(138 letters)
>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double
chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces
cerevisiae}
Length = 800
Score = 193 bits (493), Expect = 5e-59
Identities = 67/124 (54%), Positives = 85/124 (68%), Gaps = 1/124 (0%)
Query: 16 DDLVVESGKLKKLDEILPDLKKNGHRVLIFSQFIFVLDILGHYMDIRGWRHLRLDGATQV 75
L++ SGK+ LD++L LKK+GHRVLIFSQ + +LDILG Y+ I+G RLDG
Sbjct: 549 RGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPS 608
Query: 76 SSRQELIDEYNR-DQDLFAFLLSTKAGGLGINLTAADTVIIHDVDFNPYNDKQAEDRCHR 134
+ R+ ID +N D + F FLLST+AGGLGINL ADTV+I D D+NP D QA R HR
Sbjct: 609 AQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHR 668
Query: 135 VGQT 138
+GQ
Sbjct: 669 IGQK 672
>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 = 179 bits (456), Expect = 2e-54
Identities = 43/129 (33%), Positives = 68/129 (52%), Gaps = 2/129 (1%)
Query: 12 YKVPDDLVVESGKLKKLDEILPDLKKN-GHRVLIFSQFIFVLDILGHYMDIRGWRHLRLD 70
Y SGK+ LD IL + +V++ S + LD+ R + ++RLD
Sbjct: 388 YSTKAVEPQLSGKMLVLDYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLD 447
Query: 71 GATQVSSRQELIDEYNR-DQDLFAFLLSTKAGGLGINLTAADTVIIHDVDFNPYNDKQAE 129
G + R ++++ +N F F+LS+KAGG G+NL A+ +++ D D+NP ND+QA
Sbjct: 448 GTMSIKKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAM 507
Query: 130 DRCHRVGQT 138
R R GQ
Sbjct: 508 ARVWRDGQK 516
>1z5z_A Helicase of the SNF2/RAD54 family; hydrolase, recombination,
hydrolase-recombination complex; 2.00A {Sulfolobus
solfataricus} SCOP: c.37.1.19
Length = 271
Score = 141 bits (358), Expect = 5e-43
Identities = 46/140 (32%), Positives = 74/140 (52%), Gaps = 2/140 (1%)
Query: 1 MALKQT-LDCAKYKVPDDLVVESGKLKKLDEILPDLKKNGHRVLIFSQFIFVLDILGHYM 59
+ LKQ A K + V SGK+ + EI+ + G ++ IF+QF+ + I+ + +
Sbjct: 73 LKLKQIVDHPALLKGGEQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNII 132
Query: 60 DIR-GWRHLRLDGATQVSSRQELIDEYNRDQDLFAFLLSTKAGGLGINLTAADTVIIHDV 118
+ L G R ++I ++ + + +LS KAGG GINLT+A+ VI D
Sbjct: 133 EKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDR 192
Query: 119 DFNPYNDKQAEDRCHRVGQT 138
+NP + QA DR +R+GQT
Sbjct: 193 WWNPAVEDQATDRVYRIGQT 212
>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 = 143 bits (362), Expect = 1e-41
Identities = 46/140 (32%), Positives = 74/140 (52%), Gaps = 2/140 (1%)
Query: 1 MALKQT-LDCAKYKVPDDLVVESGKLKKLDEILPDLKKNGHRVLIFSQFIFVLDILGHYM 59
+ LKQ A K + V SGK+ + EI+ + G ++ IF+QF+ + I+ + +
Sbjct: 302 LKLKQIVDHPALLKGGEQSVRRSGKMIRTMEIIEEALDEGDKIAIFTQFVDMGKIIRNII 361
Query: 60 DIR-GWRHLRLDGATQVSSRQELIDEYNRDQDLFAFLLSTKAGGLGINLTAADTVIIHDV 118
+ L G R ++I ++ + + +LS KAGG GINLT+A+ VI D
Sbjct: 362 EKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVKAGGFGINLTSANRVIHFDR 421
Query: 119 DFNPYNDKQAEDRCHRVGQT 138
+NP + QA DR +R+GQT
Sbjct: 422 WWNPAVEDQATDRVYRIGQT 441
>3hgt_A HDA1 complex subunit 3; RECA-like domain, SWI2/SNF2 helical domain,
chromatin regulator, coiled coil, nucleus, repressor,
transcription; 2.20A {Saccharomyces cerevisiae} PDB:
3hgq_A
Length = 328
Score = 109 bits (273), Expect = 5e-30
Identities = 23/129 (17%), Positives = 42/129 (32%), Gaps = 11/129 (8%)
Query: 14 VPDDLVVESGKLKKLDEILPDLKKNGHRVLIFSQFIFVLDILGHYMDIRGWRHLRLDGAT 73
VP L SGK L +++ +++ I + +D+L + R DG +
Sbjct: 100 VPAHLAENSGKFSVLRDLINLVQEYETETAIVCRPGRTMDLLEALLLGNKVHIKRYDGHS 159
Query: 74 QVSSRQELIDEYNRDQDLFAFLLSTKAGGL----GINLTAADTVIIHDVDFNPYN-DKQA 128
S+ D L S++ + D +I D + D Q
Sbjct: 160 IKSAAA------ANDFSCTVHLFSSEGINFTKYPIKSKARFDMLICLDTTVDTSQKDIQY 213
Query: 129 EDRCHRVGQ 137
+ R +
Sbjct: 214 LLQYKRERK 222
>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 = 99.4 bits (247), Expect = 2e-25
Identities = 24/118 (20%), Positives = 42/118 (35%), Gaps = 3/118 (2%)
Query: 22 SGKLKKLDEILPDLKKNGHRVLIFSQFIFVLDILGHYMDIR-GWRHLRLDGATQVSSRQE 80
+++ L L + +VL+ L + R G R + R
Sbjct: 488 DPRVEWLMGYLTSHR--SQKVLVICAKAATALQLEQVLREREGIRAAVFHEGMSIIERDR 545
Query: 81 LIDEYNRDQDLFAFLLSTKAGGLGINLTAADTVIIHDVDFNPYNDKQAEDRCHRVGQT 138
+ + LL ++ G G N A +++ D+ FNP +Q R R+GQ
Sbjct: 546 AAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHMVMFDLPFNPDLLEQRIGRLDRIGQA 603
>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 = 47.9 bits (113), Expect = 2e-07
Identities = 23/122 (18%), Positives = 49/122 (40%), Gaps = 8/122 (6%)
Query: 24 KLKKLDEILPDL--KKNGHRVLIFSQFIFVLDILGHYMDIRGWRHLRLDGATQVSSRQEL 81
K+ KL EI+ + +K ++++F+ + + + + G + R G + + L
Sbjct: 344 KMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQASKENDRGL 403
Query: 82 IDEYNRDQ-DLFA-----FLLSTKAGGLGINLTAADTVIIHDVDFNPYNDKQAEDRCHRV 135
+ D FA L++T G G+++ D V+ ++ + Q R R
Sbjct: 404 SQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPVPSAIRSIQRRGRTGRH 463
Query: 136 GQ 137
Sbjct: 464 MP 465
>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 = 41.7 bits (98), Expect = 2e-05
Identities = 18/94 (19%), Positives = 44/94 (46%), Gaps = 9/94 (9%)
Query: 22 SGKLKKLDEILPDLKKNGHRVLIFSQFIFVLDILGHYMDIRGWRHLRLDGATQVSSRQEL 81
K++KL EIL + +++IF++ ++ + I + T R+E+
Sbjct: 334 KNKIRKLREILERHR--KDKIIIFTRHNELVYRISKVFLIPA-----ITHRTSREEREEI 386
Query: 82 IDEYNRDQDLFAFLLSTKAGGLGINLTAADTVII 115
++ + + F ++S++ GI++ A+ +I
Sbjct: 387 LEGFRTGR--FRAIVSSQVLDEGIDVPDANVGVI 418
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 33.4 bits (75), Expect = 0.018
Identities = 18/123 (14%), Positives = 41/123 (33%), Gaps = 13/123 (10%)
Query: 13 KVPDDLVVESGKLKKLDEILPDLKKNGH--RVLIFSQFIFV----LDILGHYMDIRGWRH 66
V D E+ KL+ L IL + ++F + + + + + +
Sbjct: 370 SVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKP 429
Query: 67 LRLDGATQVSSRQELIDEYN-------RDQDLFAFLLSTKAGGLGINLTAADTVIIHDVD 119
L G + + + + L++T GI++ + VI+++
Sbjct: 430 GILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYV 489
Query: 120 FNP 122
N
Sbjct: 490 GNV 492
>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 = 30.4 bits (68), Expect = 0.17
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 10 AKYKVPDDLVVESGKLKKLDEILPDLKKNGHR 41
Y V + V +G L+ LD + L +
Sbjct: 1844 VNYNVENQQYVAAGDLRALDTVTNVLNFIKLQ 1875
Score = 28.1 bits (62), Expect = 1.2
Identities = 25/177 (14%), Positives = 45/177 (25%), Gaps = 81/177 (45%)
Query: 18 LVVESGKLKKLDEI-------LPDLKK------NGHRVLIFSQFIFVLDILGHYMDIRGW 64
L + + +++ + LP K+ NG + + + G + G
Sbjct: 339 LSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAK-----NLV----VSGPPQSLYGL 389
Query: 65 -RHLR----LDGATQ--VSSRQELIDEYNR--------------------DQDLFAFLLS 97
LR G Q + + + NR ++DL +S
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVS 449
Query: 98 TKAGGLGI---------NLTAADTVII-----------------------HDVDFNP 122
A + I +L I H +DF P
Sbjct: 450 FNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGP 506
Score = 27.3 bits (60), Expect = 1.8
Identities = 21/115 (18%), Positives = 35/115 (30%), Gaps = 38/115 (33%)
Query: 12 YK-VPDDLVVESGK-LKKLDEILPDLKKNGHRVLIFSQFIFVLDILGHYMDIRGWRHLRL 69
Y + DL+ S + L +L D +K + ++I W L
Sbjct: 180 YHVLVGDLIKFSAETLSELIRTTLDAEK----------------VFTQGLNILEW----L 219
Query: 70 DGATQVSSRQELIDEYNRDQDLFAFLLSTKAGGLGINLT--AADTVIIHDVDFNP 122
+ + D+D +LLS I + A V + F P
Sbjct: 220 ENPSNTP-----------DKD---YLLSIPISCPLIGVIQLAHYVVTAKLLGFTP 260
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.1 bits (64), Expect = 0.35
Identities = 7/18 (38%), Positives = 7/18 (38%), Gaps = 4/18 (22%)
Query: 21 ESGKLKKLDEIL----PD 34
E LKKL L D
Sbjct: 18 EKQALKKLQASLKLYADD 35
>4f0q_A Restriction endonuclease; cytosine methylation-dependent
endonuclease, hydrolase; 2.05A {Mycobacterium SP} PDB:
4f0p_A
Length = 456
Score = 28.4 bits (62), Expect = 0.84
Identities = 8/70 (11%), Positives = 19/70 (27%)
Query: 19 VVESGKLKKLDEILPDLKKNGHRVLIFSQFIFVLDILGHYMDIRGWRHLRLDGATQVSSR 78
+ +++L+ ++ + G S + V+ W R + A
Sbjct: 178 FCGAAIIERLEHVVQRDPETGRSFPNLSLDLAVVSGGEIDGVDFRWIDDRRNAALAAGET 237
Query: 79 QELIDEYNRD 88
E
Sbjct: 238 LRHAPESWIR 247
>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 = 28.3 bits (62), Expect = 1.1
Identities = 18/107 (16%), Positives = 35/107 (32%), Gaps = 26/107 (24%)
Query: 2 ALKQTLDCAKYK----VPDDLVVESGK-LKKLDEILPDLKKNGHRVLIFSQFIFVLDILG 56
L++ L Y+ V + V++ K + ++L+ ++F V D L
Sbjct: 233 ELRRLLKSKPYENCLLVLLN--VQNAKAWNAFN--------LSCKILLTTRFKQVTDFLS 282
Query: 57 HYMDIRGWRHLRLDGATQVSSRQELIDEYNRDQDLFAFLLSTKAGGL 103
H+ LD + + E+ L L + L
Sbjct: 283 ----AATTTHISLDHHSMTLTPDEVK-------SLLLKYLDCRPQDL 318
>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics,
structural genomic consortium, SGC, hydrolase; 2.60A
{Homo sapiens}
Length = 191
Score = 26.4 bits (59), Expect = 3.0
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 19 VVESGKLKKLDEILPDLKKNGHRVLIFSQFIFVLDILGHYMDIRGWR 65
V E K+ L E L +K VLIF++ +D + Y+ ++G
Sbjct: 37 VKEEAKMVYLLECL---QKTPPPVLIFAEKKADVDAIHEYLLLKGVE 80
>3nm6_B MTA/SAH nucleosidase; hydrolase; HET: ADE; 1.60A {Helicobacter
pylori} PDB: 3nm5_A* 3nm4_A*
Length = 230
Score = 26.2 bits (58), Expect = 3.7
Identities = 11/54 (20%), Positives = 22/54 (40%), Gaps = 11/54 (20%)
Query: 79 QELIDEYNRDQDLFAFLLST-KAGGLGINLTAADTVII-----HDVDFNPYNDK 126
+I + + +L + AG L +L D ++ HDVD + ++
Sbjct: 62 TSMILAFGVQK-----VLFSGVAGSLVKDLKINDLLVATQLVQHDVDLSAFDHP 110
>2ciw_A Chloroperoxidase; oxidoreductase, heme, iron, chloride, manganese,
pyrrolidone carboxylic acid, glycoprotein,
metal-binding; HET: NAG BMA MAN HEM; 1.15A
{Caldariomyces fumago} SCOP: a.39.3.1 a.39.3.1 PDB:
1cpo_A* 2civ_A* 2cix_A* 2ciy_A* 2ciz_A* 2cj0_A* 2cj1_A*
2cj2_A* 2cpo_A* 2j18_A* 2j19_A* 2j5m_A*
Length = 299
Score = 26.5 bits (57), Expect = 3.9
Identities = 13/62 (20%), Positives = 19/62 (30%), Gaps = 1/62 (1%)
Query: 50 FVLDILGHYMDIRGWRHL-RLDGATQVSSRQELIDEYNRDQDLFAFLLSTKAGGLGINLT 108
L +L R D V++ + ID N D + F L AG +
Sbjct: 93 VNLTLLAEPHAFEHDHSFSRKDYKQGVANSNDFIDNRNFDAETFQTSLDVVAGKTHFDYA 152
Query: 109 AA 110
Sbjct: 153 DM 154
>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene
regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP:
c.22.1.1
Length = 225
Score = 25.5 bits (56), Expect = 5.7
Identities = 17/45 (37%), Positives = 22/45 (48%)
Query: 1 MALKQTLDCAKYKVPDDLVVESGKLKKLDEILPDLKKNGHRVLIF 45
AL K V DDL +E K K L EIL +L+ + + LI
Sbjct: 111 SALSVKYRENKLLVLDDLKLERPKTKSLKEILQNLQLSDKKTLIV 155
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
0.323 0.141 0.418
Gapped
Lambda K H
0.267 0.0440 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,221,155
Number of extensions: 131151
Number of successful extensions: 426
Number of sequences better than 10.0: 1
Number of HSP's gapped: 415
Number of HSP's successfully gapped: 37
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.5 bits)