RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 026552
(237 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-71
Identities = 91/227 (40%), Positives = 132/227 (58%), Gaps = 13/227 (5%)
Query: 12 SNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGD 71
+ GWA+D++ P +S ML + K NLN +SHD+A GLI L+ + +T+V++DTVG
Sbjct: 87 GDFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGM 146
Query: 72 AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 131
E YQA+L Q FP I+ V KADSL+PVVS ASI AKV RD+ ++ W F E +++ +
Sbjct: 147 PETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSD 206
Query: 132 FGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLWESDEMDEDVSS 190
+GSGYP DP+TKAWL H +FGFP VRFSW T + K+ +V+WE E +ED
Sbjct: 207 YGSGYPNDPKTKAWLRKHVDPVFGFPQFVRFSWSTAQAILEKEAEDVIWEDSEAEED--- 263
Query: 191 RRSGKRQLKLSDIGFSSSKRRSEEIESSGKGRCKFLEARKLEQLTHF 237
+R K++ + + ++ + R LE +
Sbjct: 264 ---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 = 154 bits (391), Expect = 5e-47
Identities = 50/178 (28%), Positives = 82/178 (46%), Gaps = 23/178 (12%)
Query: 17 WAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRV---LNIGILLTEVYLDTVGD-- 71
I++ E++ M N INLN+I ++ + + LNI E+Y+D
Sbjct: 62 VEKRILEAEEINQLM---NSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNT 118
Query: 72 -------AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEET 124
+K + + +R +IK + KAD+ YPVVS ASI+AK RD + +
Sbjct: 119 KKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYY----- 173
Query: 125 AENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDI--VEVLWE 180
+ ++ + GSGYP DP+T +L D+ P + R W TC +++ E
Sbjct: 174 -KKIYGDIGSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTCKRILDKSKQTKLIIE 230
>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 = 141 bits (359), Expect = 4e-42
Identities = 42/152 (27%), Positives = 65/152 (42%), Gaps = 15/152 (9%)
Query: 16 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 75
V + P L +M K +NEI + +I R+ Y+D+ +
Sbjct: 78 RTEVLKVSPENLDERMAAKT---INEILKECYAEIILRLK-----PEIAYVDSPDVIPER 129
Query: 76 QAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSG 135
++ + ++ V KAD YP+V+ ASI+AKV R+R + + +FGSG
Sbjct: 130 LSRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREIERL------KEKFGDFGSG 183
Query: 136 YPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
Y DP T+ L + PS VR W T
Sbjct: 184 YASDPRTREVLKEWIA-SGRIPSCVRMRWKTV 214
>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 = 140 bits (355), Expect = 9e-42
Identities = 47/167 (28%), Positives = 75/167 (44%), Gaps = 20/167 (11%)
Query: 12 SNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVG- 70
+ + + P + ++ LNE + + ++ + +Y D
Sbjct: 58 GVLDDYVILELPPDVIGSRE-----GTLNEFEVE---NFAKALNSLKVKPDVIYADAADV 109
Query: 71 DAEKYQAKLSQRFP-SIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMH 129
D E++ +L +R + V KAD ++PVVS ASI+AKVTRDR + + +
Sbjct: 110 DEERFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAVEKL------KEEY 163
Query: 130 RNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVE 176
GSGYP DP T+A+L ++ FP +VR W T K I E
Sbjct: 164 GEIGSGYPSDPRTRAFLENYYREHGEFPPIVRKGWKTL----KKIAE 206
>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid
ribonucleotidohydrolase, hydrolase; 2.00A {Pyrococcus
horikoshii} SCOP: c.55.3.1
Length = 220
Score = 140 bits (354), Expect = 1e-41
Identities = 48/174 (27%), Positives = 83/174 (47%), Gaps = 21/174 (12%)
Query: 16 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 75
+ V ++ P+E+ + ++NE+ + + + ++ I ++Y+D+ K
Sbjct: 62 DYYVLLVTPKEIDERH-----HSMNELEAE---KFVVALNSLRIKPQKIYVDSADVDPKR 113
Query: 76 QAKLSQRFP--SIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 133
A L + + KAD+ Y +VS ASI+AKVTRDR + + + FG
Sbjct: 114 FASLIKAGLKYEATVIAEHKADAKYEIVSAASIIAKVTRDREIEKL------KQKYGEFG 167
Query: 134 SGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDIVEVLWESDEMDED 187
SGYP DP TK WL ++ FP +VR +W T + I E + +++ D
Sbjct: 168 SGYPSDPRTKEWLEEYYKQYGDFPPIVRRTWETA----RKIEER-FRKNQLTLD 216
>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase; 2.10A
{Geobacillus stearothermophilus} PDB: 2d0a_A 2d0c_A
3asm_A
Length = 310
Score = 101 bits (253), Expect = 8e-26
Identities = 21/162 (12%), Positives = 49/162 (30%), Gaps = 9/162 (5%)
Query: 9 KWASNPFGWAVDIIDPRELSAKM-LNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLD 67
AV ++D + + + + + H+ + + + + +D
Sbjct: 144 PAIMETVPHAVTVLDNPQYNRWQRSGMPQTKMKALLHNRTLVKLVDAIA-PAEPEAIIID 202
Query: 68 TVGDAEKYQAKLSQ--RFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETA 125
+ Y LS R + KA+S++ V+ ASI+A+ + A
Sbjct: 203 EFLKRDSYFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIARYVFLEEMEQL---SRA 259
Query: 126 ENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
+ G+G D + + + +
Sbjct: 260 VGLLLPKGAGAIVDEAAARII--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 = 41.0 bits (97), Expect = 1e-04
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 93 KADSLYPVVSGASIVAKVTRDR 114
K D ++ ASIVAKV RDR
Sbjct: 134 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 = 37.1 bits (85), Expect = 0.005
Identities = 38/245 (15%), Positives = 76/245 (31%), Gaps = 83/245 (33%)
Query: 14 PFGWAVDIIDPRELSAKMLNKNKIN--LNEISHDSAIGLITRVLNIGILLTEVYLDTVGD 71
F D D +++ +L+K +I+ + S T L LL+
Sbjct: 28 AFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG----TLRL-FWTLLS--------- 73
Query: 72 AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 131
Q ++ Q+F V + Y + S + R ++ ++ E + ++ +
Sbjct: 74 ---KQEEMVQKF------VEEVLRINYKFL--MSPIKTEQRQPSMMTRMYIEQRDRLYND 122
Query: 132 ------------------------------------FGSGYPGDPETKAWLT-----DHK 150
GSG K W+ +K
Sbjct: 123 NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSG-------KTWVALDVCLSYK 175
Query: 151 HIIFGFPSLVRFSW---GTCTSHFKDIVEVLWE-SDEMDEDVSSRRSGKRQLKLSDIGFS 206
+ + F W C S + ++E+L + ++D + +SR +KL
Sbjct: 176 -VQCKMDFKI-F-WLNLKNCNSP-ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ 231
Query: 207 SSKRR 211
+ RR
Sbjct: 232 AELRR 236
Score = 36.4 bits (83), Expect = 0.008
Identities = 29/232 (12%), Positives = 60/232 (25%), Gaps = 73/232 (31%)
Query: 17 WAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNI-----GILLTEVYLD---- 67
+ LS K+L L TR + T + LD
Sbjct: 254 QNAKAWNAFNLSCKIL-----------------LTTRFKQVTDFLSAATTTHISLDHHSM 296
Query: 68 --TVGDAEKYQAK-LSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIF--E 122
T + + K L R + ++ + P SI+A+ RD W
Sbjct: 297 TLTPDEVKSLLLKYLDCRPQDLP----REVLTTNPRR--LSIIAESIRDGLAT-WDNWKH 349
Query: 123 ETAENMHRNFGSGYPG-DPETKAWLTDHKHIIFGFPSLVRFSWGTCTSHFKDI------V 175
+ + S +P +++ + F L F +
Sbjct: 350 VNCDKLTTIIESSLNVLEPA------EYRKM---FDRLSVFP--------PSAHIPTILL 392
Query: 176 EVLWESDE-------MDEDVSS----RRSGKRQLKLSDIGFSSSKRRSEEIE 216
++W +++ ++ + + + I + E
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA 444
>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 = 27.7 bits (61), Expect = 4.6
Identities = 24/126 (19%), Positives = 36/126 (28%), Gaps = 46/126 (36%)
Query: 5 AALPKWASNPF--------------GWAVDIIDPR-ELSAKMLNKNKINLNEISHDSAIG 49
A W S F G P L +L E S ++ G
Sbjct: 284 AETDSWES--FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSIL--------EDSLENNEG 333
Query: 50 LITRVLNI-GILLTEVYLDTVGDAEKYQAKLSQRFP-----SI-------KFVVSKKADS 96
+ + +L+I + +V + Y K + P I VVS S
Sbjct: 334 VPSPMLSISNLTQEQV--------QDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQS 385
Query: 97 LYPVVS 102
LY +
Sbjct: 386 LYGLNL 391
>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 = 26.5 bits (58), Expect = 9.0
Identities = 8/41 (19%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 106 IVAKVTRDRTLRGW-IFEETAENMHRNFGSGYPGDPETKAW 145
+ 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 0.133 0.396
Gapped
Lambda K H
0.267 0.0586 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,662,341
Number of extensions: 213390
Number of successful extensions: 450
Number of sequences better than 10.0: 1
Number of HSP's gapped: 435
Number of HSP's successfully gapped: 14
Length of query: 237
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 146
Effective length of database: 4,160,982
Effective search space: 607503372
Effective search space used: 607503372
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: 56 (25.7 bits)