RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 030402
(178 letters)
>3kio_A Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse H2,
protein complex, autoimmune disease, endonuclease,
hydrolase, metal-binding; 2.90A {Mus musculus} PDB:
3p5j_A 3puf_A 3p56_A
Length = 301
Score = 218 bits (558), Expect = 3e-72
Identities = 86/163 (52%), Positives = 109/163 (66%), Gaps = 1/163 (0%)
Query: 8 PKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFE 67
PC++G+DEAGRGPVLGPMVY YCP S L L ADSKTL E +RE LF
Sbjct: 22 AVCLKEPCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFA 81
Query: 68 DLKVN-DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYL 126
++ + D VGWA+D++ P +S ML + K NLN +SHD+A GLI L+ + +T+V++
Sbjct: 82 KMEEDGDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFV 141
Query: 127 DTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
DTVG E YQA+L Q FP I+ V KADSL+PVVS ASI AK
Sbjct: 142 DTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAK 184
>1eke_A Ribonuclease HII; endonuclease, structural genomics, BSGC structure
funded by NIH, protein structure initiative, PSI; HET:
MES; 2.00A {Methanocaldococcus jannaschii} SCOP:
c.55.3.1
Length = 230
Score = 169 bits (429), Expect = 1e-53
Identities = 58/166 (34%), Positives = 84/166 (50%), Gaps = 17/166 (10%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
I+GIDEAGRGPVLGPMV ++ L L DSK L + KR L + L+ +
Sbjct: 3 IIGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLE--NLG 60
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRV---LNIGILLTEVYLDTVGD- 131
I++ E++ M N INLN+I ++ + + LNI E+Y+D
Sbjct: 61 YVEKRILEAEEINQLM---NSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTN 117
Query: 132 --------AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
+K + + +R +IK + KAD+ YPVVS ASI+AK
Sbjct: 118 TKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAK 163
>1i39_A Ribonuclease HII, RNAse HII; mixed beta sheet, helix-loop-helix,
hydrolase; 1.95A {Archaeoglobus fulgidus} SCOP: c.55.3.1
PDB: 1i3a_A 3p83_D*
Length = 225
Score = 164 bits (418), Expect = 6e-52
Identities = 47/157 (29%), Positives = 75/157 (47%), Gaps = 12/157 (7%)
Query: 13 NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN 72
+ GIDEAG+G V+GP+V + C + L L DSK L + +REEL E+++
Sbjct: 19 SHMKAGIDEAGKGCVIGPLVVAGVACS--DEDRLRKLGVKDSKKLSQGRREELAEEIR-- 74
Query: 73 DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
V + P L +M K +NEI + +I R+ Y+D+
Sbjct: 75 KICRTEVLKVSPENLDERMAAKT---INEILKECYAEIILRLK-----PEIAYVDSPDVI 126
Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
+ ++ + ++ V KAD YP+V+ ASI+AK
Sbjct: 127 PERLSRELEEITGLRVVAEHKADEKYPLVAAASIIAK 163
>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid
ribonucleotidohydrolase, hydrolase; 2.00A {Pyrococcus
horikoshii} SCOP: c.55.3.1
Length = 220
Score = 162 bits (411), Expect = 6e-51
Identities = 45/156 (28%), Positives = 77/156 (49%), Gaps = 11/156 (7%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
+ G+DEAGRGPV+GP+V G + L + DSK L +RE+LF L +
Sbjct: 3 VAGVDEAGRGPVIGPLVIGVAVIDEKNIERLRDIGVKDSKQLTPGQREKLFSKLI-DILD 61
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
+ V ++ P+E+ + ++NE+ + + + ++ I ++Y+D+ K
Sbjct: 62 DYYVLLVTPKEIDERH-----HSMNELEAE---KFVVALNSLRIKPQKIYVDSADVDPKR 113
Query: 136 QAKLSQRFP--SIKFVVSKKADSLYPVVSGASIVAK 169
A L + + KAD+ Y +VS ASI+AK
Sbjct: 114 FASLIKAGLKYEATVIAEHKADAKYEIVSAASIIAK 149
>1io2_A Ribonuclease HII; endonuclease, hydrolase; 2.00A {Thermococcus
kodakarensis} SCOP: c.55.3.1 PDB: 2dfh_A 2dff_A 2dfe_A
1x1p_A
Length = 213
Score = 161 bits (410), Expect = 6e-51
Identities = 48/156 (30%), Positives = 76/156 (48%), Gaps = 11/156 (7%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
I GIDEAGRGPV+GPMV + + L L DSK L ++RE+LF ++
Sbjct: 3 IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEIL-GVLD 61
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEK 134
+ + + P + ++ LNE + + ++ + +Y D D E+
Sbjct: 62 DYVILELPPDVIGSRE-----GTLNEFEVE---NFAKALNSLKVKPDVIYADAADVDEER 113
Query: 135 YQAKLSQRFP-SIKFVVSKKADSLYPVVSGASIVAK 169
+ +L +R + V KAD ++PVVS ASI+AK
Sbjct: 114 FARELGERLNFEAEVVAKHKADDIFPVVSAASILAK 149
>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A
{Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A
3asm_A
Length = 310
Score = 143 bits (361), Expect = 1e-42
Identities = 35/170 (20%), Positives = 67/170 (39%), Gaps = 6/170 (3%)
Query: 3 SEAALPKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKR 62
A + +G DE G G GP+V Y + +A L DSK L +E
Sbjct: 80 PSALAAHQLGSLSAIGSDEVGTGDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAI 139
Query: 63 EELFEDLKVNDSVGWAVDIIDPRELSAKM-LNKNKINLNEISHDSAIGLITRVLNIGILL 121
+ + + ++V AV ++D + + + + + H+ + + +
Sbjct: 140 KRIAPAIM--ETVPHAVTVLDNPQYNRWQRSGMPQTKMKALLHNRTLVKLVDAIA-PAEP 196
Query: 122 TEVYLDTVGDAEKYQAKLSQ--RFPSIKFVVSKKADSLYPVVSGASIVAK 169
+ +D + Y LS R + KA+S++ V+ ASI+A+
Sbjct: 197 EAIIIDEFLKRDSYFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIAR 246
>2etj_A Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC 3.1.26.4)
(RNAse HII), structur genomics, joint center for
structural genomics; 1.74A {Thermotoga maritima} SCOP:
c.55.3.1 PDB: 3o3g_A* 3o3f_A* 3o3h_A*
Length = 250
Score = 59.5 bits (145), Expect = 2e-11
Identities = 36/154 (23%), Positives = 60/154 (38%), Gaps = 29/154 (18%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
+ G+DEAGRG + GP+V + DSK L KRE L +++ +
Sbjct: 26 VAGVDEAGRGCLAGPVVAAAVVLEKEI------EGINDSKQLSPAKRERLLDEIMEKAA- 78
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
+ I P E+ + N I + + + + + N+ + + V +D
Sbjct: 79 -VGIGIASPEEI-------DLYN---IFNATKLAMNRALENLSVKPSFVLVDGK------ 121
Query: 136 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAK 169
+ P V K D ++ ASIVAK
Sbjct: 122 --GIELSVPGTCLV---KGDQKSKLIGAASIVAK 150
>3qb0_A Actin-related protein 4; actin fold, ATP binding, nucleus,
structural protein; HET: ATP; 3.40A {Saccharomyces
cerevisiae}
Length = 498
Score = 28.4 bits (63), Expect = 1.2
Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 130 GDAEKYQAKLSQRFPSIKFVV---SKKADSLYPVVSGASIVAKRSNFERM 176
G +++ +L++ PS+KF + + Y G SI+ F ++
Sbjct: 428 GLSDRLMTELNKILPSLKFRILTTGHTIERQYQSWLGGSILTSLGTFHQL 477
>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 = 28.5 bits (63), Expect = 1.4
Identities = 22/112 (19%), Positives = 35/112 (31%), Gaps = 37/112 (33%)
Query: 65 LFEDLKVNDSVGWAVDIIDPR-ELSAKMLNKNKINLNEISHDSAIGLITRVLNI-GILLT 122
LF +G P L +L E S ++ G+ + +L+I +
Sbjct: 303 LF-------FIGVRCYEAYPNTSLPPSIL--------EDSLENNEGVPSPMLSISNLTQE 347
Query: 123 EVYLDTVGDAEKYQAKLSQRFP-----SI-------KFVVSKKADSLYPVVS 162
+V + Y K + P I VVS SLY +
Sbjct: 348 QV--------QDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNL 391
>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 = 27.9 bits (61), Expect = 2.1
Identities = 11/67 (16%), Positives = 22/67 (32%), Gaps = 13/67 (19%)
Query: 55 KTLKEEKREELFEDLKV-NDSVG---------WA-VDIIDPRELSAKMLNKNKINLNEIS 103
L+ + ++F+ L V S W V D + K+ + +
Sbjct: 364 NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ--P 421
Query: 104 HDSAIGL 110
+S I +
Sbjct: 422 KESTISI 428
>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain,
ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora
crassa}
Length = 443
Score = 26.9 bits (60), Expect = 3.9
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 39 PCSYQQTLATLNFAD 53
P Y +TL+TL +AD
Sbjct: 394 PTDYDETLSTLRYAD 408
>1t5c_A CENP-E protein, centromeric protein E; kinesin motor-domain-ADP
complex, stranded beta-sheet core with solvent exposed
alpha-helices; HET: ADP PIN; 2.50A {Homo sapiens}
Length = 349
Score = 26.8 bits (60), Expect = 4.0
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 39 PCSYQQTLATLNFAD 53
P S+ +TL L FA
Sbjct: 309 PVSFDETLTALQFAS 323
>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein
binding; 1.45A {Gallus gallus} SCOP: c.10.1.1
Length = 185
Score = 26.5 bits (59), Expect = 4.0
Identities = 21/103 (20%), Positives = 34/103 (33%), Gaps = 30/103 (29%)
Query: 45 TLATLNFADSKTLKEEKREELFEDLKVNDSVGWAVDIIDPRELS--------------AK 90
L +N + + + E LK N V ++ S A+
Sbjct: 37 DLEEVNLNNIMNIPVPTLKACAEALKTNTYV---------KKFSIVGTRSNDPVAFALAE 87
Query: 91 MLNKNK----INL--NEISHDSAIGLITRVLNIGILLTEVYLD 127
ML N +N+ N IS + L+ L L E+ +D
Sbjct: 88 MLKVNNTLKSLNVESNFISGSGILALV-EALQSNTSLIELRID 129
>2xhg_A Tyrocidine synthetase A; isomerase, nonribosomal peptide synthesis,
cofactor-independ epimerization; 1.50A {Brevibacillus
brevis}
Length = 466
Score = 26.5 bits (59), Expect = 5.2
Identities = 7/16 (43%), Positives = 10/16 (62%)
Query: 62 REELFEDLKVNDSVGW 77
RE++ E V +VGW
Sbjct: 290 REDIIEQANVARTVGW 305
>1pgv_A TMD-1, tropomodulin TMD-1; structural genomics, PSI, protein
structure initiative, southeast collaboratory for
structural genomics secsg; 1.80A {Caenorhabditis
elegans} SCOP: c.10.1.1
Length = 197
Score = 25.6 bits (56), Expect = 9.1
Identities = 11/78 (14%), Positives = 28/78 (35%), Gaps = 11/78 (14%)
Query: 45 TLATLNFADSKTLKEEKREELFEDLKVNDSVGW----AVDIIDPRELS-AKMLNKNK--- 96
L +N + K + +E+ L E + + I D +++ +
Sbjct: 42 DLKEVNINNMKRVSKERIRSLIEAACNSKHIEKFSLANTAISDSEARGLIELIETSPSLR 101
Query: 97 -INL--NEISHDSAIGLI 111
+N+ N ++ + L+
Sbjct: 102 VLNVESNFLTPELLARLL 119
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 0.134 0.389
Gapped
Lambda K H
0.267 0.0561 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,584,671
Number of extensions: 141209
Number of successful extensions: 300
Number of sequences better than 10.0: 1
Number of HSP's gapped: 285
Number of HSP's successfully gapped: 16
Length of query: 178
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 91
Effective length of database: 4,272,666
Effective search space: 388812606
Effective search space used: 388812606
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: 54 (25.0 bits)