RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 022427
(297 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 = 317 bits (815), Expect = e-109
Identities = 127/292 (43%), Positives = 174/292 (59%), Gaps = 14/292 (4%)
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 DTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAE 186
DTVG E YQA+L Q FP I+ V KADSL+PVVS ASI AKV RD+ ++ W F E +
Sbjct: 142 DTVGMPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQ 201
Query: 187 NMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLWESDEMD 245
++ ++GSGYP DP+TKAWL H +FGFP VRFSW T + K+ +V+WE E +
Sbjct: 202 DLDSDYGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDVIWEDSEAE 261
Query: 246 EDVSSRRSGKRQLKLSDIGFSSSKRRSEEIESSGKGRCKFLEARKLEQLTHF 297
ED +R K++ + + ++ + R LE +
Sbjct: 262 ED------PERPGKITSYFSQGPQTCRPQA------PHRYFQERGLEAASSL 301
>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 = 241 bits (618), Expect = 3e-80
Identities = 76/239 (31%), Positives = 115/239 (48%), Gaps = 25/239 (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 --------AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEE 183
+K + + +R +IK + KAD+ YPVVS ASI+AK RD + +
Sbjct: 118 TKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYY---- 173
Query: 184 TAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDI--VEVLWE 240
+ ++ + GSGYP DP+T +L D+ P + R W TC +++ E
Sbjct: 174 --KKIYGDIGSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTCKRILDKSKQTKLIIE 230
>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid
ribonucleotidohydrolase, hydrolase; 2.00A {Pyrococcus
horikoshii} SCOP: c.55.3.1
Length = 220
Score = 227 bits (582), Expect = 6e-75
Identities = 71/234 (30%), Positives = 115/234 (49%), Gaps = 22/234 (9%)
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--SIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
A L + + KAD+ Y +VS ASI+AKVTRDR + + + FG
Sbjct: 114 FASLIKAGLKYEATVIAEHKADAKYEIVSAASIIAKVTRDREIEKL------KQKYGEFG 167
Query: 194 SGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWESDEMDED 247
SGYP DP TK WL ++ FP +VR +W T + I E + +++ D
Sbjct: 168 SGYPSDPRTKEWLEEYYKQYGDFPPIVRRTWETA----RKIEER-FRKNQLTLD 216
>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 = 227 bits (581), Expect = 6e-75
Identities = 72/223 (32%), Positives = 108/223 (48%), Gaps = 21/223 (9%)
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-SIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 193
+ +L +R + V KAD ++PVVS ASI+AKVTRDR + + + G
Sbjct: 114 FARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAVEKL------KEEYGEIG 167
Query: 194 SGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVE 236
SGYP DP T+A+L ++ FP +VR W T K I E
Sbjct: 168 SGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTL----KKIAE 206
>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 = 224 bits (573), Expect = 2e-73
Identities = 65/219 (29%), Positives = 98/219 (44%), Gaps = 20/219 (9%)
Query: 10 WASN-PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFED 68
GIDEAG+G V+GP+V + C + L L DSK L + +REEL E+
Sbjct: 15 VPRGSHMKAGIDEAGKGCVIGPLVVAGVACS--DEDRLRKLGVKDSKKLSQGRREELAEE 72
Query: 69 LKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDT 128
++ V + P L +M K +NEI + +I R+ Y+D+
Sbjct: 73 IR--KICRTEVLKVSPENLDERMAAKT---INEILKECYAEIILRLK-----PEIAYVDS 122
Query: 129 VGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENM 188
+ ++ + ++ V KAD YP+V+ ASI+AKV R+R + +
Sbjct: 123 PDVIPERLSRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREIERL------KEK 176
Query: 189 HRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227
+FGSGY DP T+ L + PS VR W T
Sbjct: 177 FGDFGSGYASDPRTREVLKEWIA-SGRIPSCVRMRWKTV 214
>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A
{Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A
3asm_A
Length = 310
Score = 182 bits (462), Expect = 7e-56
Identities = 39/228 (17%), Positives = 78/228 (34%), Gaps = 11/228 (4%)
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--RFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGW 179
+ +D + Y LS R + KA+S++ V+ ASI+A+ +
Sbjct: 197 EAIIIDEFLKRDSYFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIARYVFLEEMEQL 256
Query: 180 IFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 227
A + G+G D + + + +
Sbjct: 257 ---SRAVGLLLPKGAGAIVDEAAARII--RARGEEMLETCAKLHFANT 299
>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 = 74.6 bits (184), Expect = 8e-16
Identities = 40/159 (25%), Positives = 64/159 (40%), Gaps = 29/159 (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 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174
+ P V K D ++ ASIVAKV RDR
Sbjct: 122 --GIELSVPGTCLV---KGDQKSKLIGAASIVAKVFRDR 155
>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 = 40.2 bits (93), Expect = 8e-04
Identities = 41/255 (16%), Positives = 82/255 (32%), Gaps = 88/255 (34%)
Query: 64 ELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKIN--LNEISHDSAIGLITRVLNIGILL 121
+FED V++ D D +++ +L+K +I+ + S T L LL
Sbjct: 23 SVFEDAFVDN-----FDCKDVQDMPKSILSKEEIDHIIMSKDAVSG----TLRL-FWTLL 72
Query: 122 TEVYLDTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIF 181
+ Q ++ Q+F V + Y + S + R ++ ++
Sbjct: 73 S------------KQEEMVQKF------VEEVLRINYKFL--MSPIKTEQRQPSMMTRMY 112
Query: 182 EETAENMHRN------------------------------------FGSGYPGDPETKAW 205
E + ++ + GSG K W
Sbjct: 113 IEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSG-------KTW 165
Query: 206 LT-----DHKHIIFGFPSLVRFSW---GTCTSHFKDIVEVLWE-SDEMDEDVSSRRSGKR 256
+ +K + + F W C S + ++E+L + ++D + +SR
Sbjct: 166 VALDVCLSYK-VQCKMDFKI-F-WLNLKNCNSP-ETVLEMLQKLLYQIDPNWTSRSDHSS 221
Query: 257 QLKLSDIGFSSSKRR 271
+KL + RR
Sbjct: 222 NIKLRIHSIQAELRR 236
Score = 38.3 bits (88), Expect = 0.003
Identities = 31/254 (12%), Positives = 74/254 (29%), Gaps = 78/254 (30%)
Query: 55 KTLKEEKREELFEDLKV-NDSVG---------WA-VDIIDPRELSAKMLNKNKINLNE-- 101
L+ + ++F+ L V S W V D + K+ + +
Sbjct: 364 NVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423
Query: 102 --IS-HDSAIGLITRVLNIGIL---LTEVY---------------------------LDT 128
IS + L ++ N L + + Y L
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKN 483
Query: 129 VGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENM 188
+ E+ F +F+ K + SI+ + + + + +I +
Sbjct: 484 IEHPERM-TLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDN----- 537
Query: 189 HRNFGSGYPGDPETKAWLTDHKHIIFGF-PSLVRFSWGTCTSHFKDIVEV--LWESDEMD 245
DP+ + + + +L+ S + D++ + + E + +
Sbjct: 538 ----------DPKYERLVNAILDFLPKIEENLIC-------SKYTDLLRIALMAEDEAIF 580
Query: 246 EDVSSRRSGKRQLK 259
E+ +Q++
Sbjct: 581 EEAH------KQVQ 588
Score = 27.5 bits (60), Expect = 6.5
Identities = 26/169 (15%), Positives = 55/169 (32%), Gaps = 52/169 (30%)
Query: 39 PCSYQQTLATLNFADS----------KTLKEEKREELFEDLKVNDSVGWAVDIIDPRELS 88
P ++ + D K ++ +R LF + ++ +
Sbjct: 456 PKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFR--FL---------- 503
Query: 89 AKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSIKF 148
+ KI + + +++ + L+T+ + Y+ + P +
Sbjct: 504 -----EQKIRHDSTAWNASGSI---------------LNTLQQLKFYKPYICDNDPKYER 543
Query: 149 VVSKKADSLYPVVSGASIVAKVTRDRTLR-------GWIFEETAENMHR 190
+V+ D L P + I +K T LR IFEE + + R
Sbjct: 544 LVNAILDFL-PKIEENLICSKYT--DLLRIALMAEDEAIFEEAHKQVQR 589
>1io0_A Tropomodulin; LRR protein, right-handed super-helix, protein
binding; 1.45A {Gallus gallus} SCOP: c.10.1.1
Length = 185
Score = 29.2 bits (66), Expect = 1.2
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
>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 = 27.5 bits (61), Expect = 4.3
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
>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 = 28.1 bits (62), Expect = 4.4
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
>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 = 8.6
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 = 8.8
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 39 PCSYQQTLATLNFAD 53
P S+ +TL L FA
Sbjct: 309 PVSFDETLTALQFAS 323
>2hq2_A Putative heme/hemoglobin transport protein; heme oxygenase,
structural repeat; HET: HEM; 1.45A {Escherichia coli}
SCOP: e.62.1.1 PDB: 1u9t_A
Length = 354
Score = 26.9 bits (59), Expect = 9.6
Identities = 8/41 (19%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 166 IVAKVTRDRTLRGW-IFEETAENMHRNFGSGYPGDPETKAW 205
+ K T D + +F + + +G G+ E W
Sbjct: 300 VTRKPTSDGYVTSLELFAHDGTQIAQLYGQRTEGEQEQAQW 340
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 0.401
Gapped
Lambda K H
0.267 0.0606 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,546,865
Number of extensions: 267898
Number of successful extensions: 550
Number of sequences better than 10.0: 1
Number of HSP's gapped: 526
Number of HSP's successfully gapped: 17
Length of query: 297
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 204
Effective length of database: 4,105,140
Effective search space: 837448560
Effective search space used: 837448560
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 (26.0 bits)