RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9180
(491 letters)
>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 = 72.4 bits (177), Expect = 2e-13
Identities = 52/278 (18%), Positives = 92/278 (33%), Gaps = 99/278 (35%)
Query: 119 LSLGKDRKNDTPSVAFQQLFAGVINSK-YANYT-ICY---TDGSK---------TMNTTS 164
S+ N+ ++ F G + NY+ + + DG ++TS
Sbjct: 1659 FSILDIVINNPVNLTI--HFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTS 1716
Query: 165 CAFSIDDLISSSQLN------PVNSIFSAELIAIYLCLEAITVHPSDQFLIVSDSR---- 214
F + L+ P ++ E A + L++ + LI +D+
Sbjct: 1717 YTFRSEK----GLLSATQFTQP--ALTLME-KAAFEDLKS-------KGLIPADATFAGH 1762
Query: 215 -----SALAALSNV-SFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRG---NEAV- 264
+ALA+L++V S L+ +VV + RG AV
Sbjct: 1763 SLGEYAALASLADVMSIE-----------SLV----EVVFY---------RGMTMQVAVP 1798
Query: 265 -DEAARNP-----VNPTQLKL-CSPEDFKPIAASIVKKEWQ-----NQWDNVPNTN---- 308
DE R+ +NP ++ S E + + + K+ N NV N
Sbjct: 1799 RDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVN--YNVENQQYVAA 1856
Query: 309 -KLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSL 345
L+A+ + N + I E+ S SL
Sbjct: 1857 GDLRALDTVTNVLNFIKLQK------IDIIELQKSLSL 1888
Score = 64.7 bits (157), Expect = 4e-11
Identities = 93/540 (17%), Positives = 160/540 (29%), Gaps = 210/540 (38%)
Query: 4 LASIIGELEELFYINCKNNNNI----EQLEEKEEVHLSLRRSKLLMNYVA---------- 49
L + E E + N+I +L ++ + L ++ +L+ NY+
Sbjct: 84 LNLCLTEFENCYL----EGNDIHALAAKLLQENDTTL-VKTKELIKNYITARIMAKRPFD 138
Query: 50 KVRASP-FNPVQK------VLFS-Q-NLTPYNF-------TTNKPKPLLSRF--QSLPSF 91
K S F V + +F Q N Y F T L+ S +
Sbjct: 139 KKSNSALFRAVGEGNAQLVAIFGGQGNTDDY-FEELRDLYQT--YHVLVGDLIKFSAETL 195
Query: 92 PNLISSSDMAPYVRT----VPPW---SSPSPPVD------LSLGKDRKNDTPSVAFQQLF 138
LI ++ A V T + W S +P D +S P + QL
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISC--------PLIGVIQL- 246
Query: 139 AGVINSKYANYTI-CYTDGSKTMNTTSCAFSIDDLISSSQLNPVNSIFSAELIAIYLCLE 197
A+Y + G P EL + L+
Sbjct: 247 --------AHYVVTAKLLG---------------------FTP------GELRSY---LK 268
Query: 198 AITVHPSDQFLIVSDSRSALA-ALSNVSFTNPLVSKVYSCWD-LLRSRNKVVHFL-WCPS 254
T H +V+ A+A A + W+ S K + L +
Sbjct: 269 GATGHSQG---LVT----AVAIAET-------------DSWESFFVSVRKAITVLFFI-- 306
Query: 255 HCGIRGNEAVDEAARNPVNPTQLKLCSPEDFKPIAASIVKKEWQNQWDNVPN-----TN- 308
G+R EA + + SI++ +N + VP+ +N
Sbjct: 307 --GVRCYEAYPNTS-------------------LPPSILEDSLENN-EGVPSPMLSISNL 344
Query: 309 KLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDHVIHSI 368
+ ++ + N+ + ++I SL N +++ +
Sbjct: 345 TQEQVQDYVNKTNSHLPAGKQ--VEI---------SL------VNGA------KNLV--V 379
Query: 369 HGIPTKSEVIIELFSEVL-LSKLH-NSGVVESR---SYTKVLLLTEFVPIMTELVPILTD 423
G P +S L+ L L K SG+ +SR S K+ F+P+
Sbjct: 380 SG-PPQS-----LYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPV--------AS 425
Query: 424 PTHRSY---TQVLLLTEFVPIMTEF------VPIL-TDPTHRYRYL--PILTELVPILTV 471
P H L+ + V F +P+ T R L I +V +
Sbjct: 426 PFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIR 485
>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 = 69.1 bits (168), Expect = 2e-12
Identities = 87/492 (17%), Positives = 155/492 (31%), Gaps = 134/492 (27%)
Query: 7 IIGELEELFY--INCKNNNNIEQLEE----KEEV-HL-----SLRRSKLLMNYVAKVRAS 54
I+ E+ F +CK+ ++ + + KEE+ H+ ++ + L + +
Sbjct: 21 ILSVFEDAFVDNFDCKD---VQDMPKSILSKEEIDHIIMSKDAVSGTLRLFW---TLLSK 74
Query: 55 PFNPVQKVLFSQNLTP-YNFTTNKPKPLLSRFQSLPSFPNLISSSDMAPYVRTVPP-WSS 112
VQK + L Y F L+S ++ P S Y+ ++
Sbjct: 75 QEEMVQK-FVEEVLRINYKF-------LMSPIKTEQRQP----SMMTRMYIEQRDRLYND 122
Query: 113 PSPPVDLSLGKDRKNDTPSVAFQQLFAGVINSKYANYTICYTD-GS-KT----------- 159
++ + + + +L ++ + A + GS KT
Sbjct: 123 NQVFAKYNVSRLQP-------YLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK 175
Query: 160 -----------MNTTSCAFSIDDLIS-----SSQLNPVNSIFSAELIAIYLCLEAITVHP 203
+N +C S + ++ Q++P + S I L + +I
Sbjct: 176 VQCKMDFKIFWLNLKNC-NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234
Query: 204 SDQFLIVSDSRSALAALSNVSFTNPLVSKVY--SCWDLLRSRNK-VVHFLWCPSHCGIRG 260
L + L L NV N + SC LL +R K V FL + I
Sbjct: 235 RR-LLKSKPYENCLLVLLNVQ--NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISL 291
Query: 261 NEAV-----DEA-------ARNPVN--PTQLKLCSPEDFKPIAASIVKKEWQNQWDNVP- 305
+ DE P ++ +P IA SI ++ WDN
Sbjct: 292 DHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI--RDGLATWDNWKH 349
Query: 306 -NTNKL-KAIKPLIAPWNTSNQENRTQEIQIKQCEIPASTSLTGYANIYNIPPIPCLIDH 363
N +KL I+ + + + + P S +IP
Sbjct: 350 VNCDKLTTIIESSLNVLEPAEYRKMFDRLSV----FPPSA---------HIPT------I 390
Query: 364 VIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESRSYTKV-------LLLTEFVPIMTE 416
++ I KS+V V+++KLH +VE + L L +
Sbjct: 391 LLSLIWFDVIKSDV------MVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA 444
Query: 417 LVPILTDPTHRS 428
L HRS
Sbjct: 445 L--------HRS 448
Score = 42.9 bits (100), Expect = 2e-04
Identities = 42/371 (11%), Positives = 101/371 (27%), Gaps = 86/371 (23%)
Query: 128 DTPSVAFQQLFAGVINSKYANY-----TICYTDGSKTMNTTSCAFSIDDLISSSQLNPVN 182
Q+ V+ NY I +M T D L + +Q+
Sbjct: 73 SKQEEMVQKFVEEVLR---INYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129
Query: 183 SIFSAELI-AIYLCLEAITVHPSDQFLIV----SDSRSALAA--LSNVSFTNPLVSKVYS 235
++ + + L + +++ ++ +A + + K++
Sbjct: 130 NVSRLQPYLKLRQALLELRPAK---NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIF- 185
Query: 236 CW----------DLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPEDF 285
W +L K+++ + D ++ + ++ +
Sbjct: 186 -WLNLKNCNSPETVLEMLQKLLYQIDPN------WTSRSDHSSNIKLRIHSIQ----AEL 234
Query: 286 KPIAASIVKKEWQNQW---DNVPNTNKLKAIKPLIAPWNTSNQENRTQEIQIKQCEIPAS 342
+ + + K ++N NV N A C+I +
Sbjct: 235 RRL---LKSKPYENCLLVLLNVQNAKAWNAFNL--------------------SCKILLT 271
Query: 343 T---SLTGYANIYNIPPIPCLIDHVIHSIHGIPTKSEVIIELFSEVLLSKLHNSGVVESR 399
T +T + + I + H + T EV L + L + + R
Sbjct: 272 TRFKQVTDFLSAATTTHIS-----LDHHSMTL-TPDEVK-SLLLKYLDCRPQD----LPR 320
Query: 400 SYTKVLLLTEFVPIMTELVPILTDPTHRSYTQVLLLTEFVPIMTEFVPILTDPTHR--YR 457
+ I+ E + + + + I+ + +L +R +
Sbjct: 321 EVLTTNPRR--LSIIAESIRD--GLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD 376
Query: 458 YLPILTELVPI 468
L + I
Sbjct: 377 RLSVFPPSAHI 387
>3p1g_A Xenotropic murine leukemia virus-related virus (X H domain; XMRV,
RNAse H, reverse transcriptase, transcription; 1.50A
{Xenotropic mulv-related virus} PDB: 3v1q_A 3v1o_A
3v1r_A* 2hb5_A
Length = 165
Score = 52.2 bits (125), Expect = 3e-08
Identities = 36/137 (26%), Positives = 52/137 (37%), Gaps = 21/137 (15%)
Query: 147 ANYTICYTDGSKTMNT----TSCAFSIDD-LISSSQLNPVNSIFSAELIAIYLCLEAITV 201
A+YT YTDGS + A + + +I + L S AELIA+ L+
Sbjct: 22 ADYTW-YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMA-- 78
Query: 202 HPSDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCW----DLLRSRNKVVHFLWCPSHCG 257
+ + +DSR A A S K + L ++ + CP H
Sbjct: 79 -EGKKLNVYTDSRYAFATAHVHSEGRE--IKNKNEILALLKALFLPKRL-SIIHCPGHQK 134
Query: 258 -----IRGNEAVDEAAR 269
RGN D+AAR
Sbjct: 135 GNSAEARGNRMADQAAR 151
>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO
enzyme, structural genomics, protein structure
initiative; NMR {Desulfitobacterium hafniense dcb-2}
PDB: 2kw4_A
Length = 147
Score = 47.3 bits (113), Expect = 1e-06
Identities = 21/126 (16%), Positives = 41/126 (32%), Gaps = 12/126 (9%)
Query: 153 YTDGSKTMNTTSCAFSI------DDLISSSQLNPVNSI---FSAELIAIYLCLEAITVHP 203
YTDGS + A++ + NP + + E+ A ++ +
Sbjct: 10 YTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAALYAVKKASQLG 69
Query: 204 SDQFLIVSDSRSALAALSNVSFTNPLVSKVYSCWDLLRSRNKVVHFLWCPSHCGIRGNEA 263
+ I+ D + ++ Y L+ + F +H G N+
Sbjct: 70 V-KIRILHDYAGIAFWATGEWKAKNEFTQAY--AKLMNQYRGIYSFEKVKAHSGNEFNDY 126
Query: 264 VDEAAR 269
VD A+
Sbjct: 127 VDMKAK 132
>2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI,
nonnucleoside inhibitor, AIDS, HIV, rilpivirine,
diarylpyrimidine, DAPY, DNA recombination; HET: T27;
1.80A {Human immunodeficiency virus 1} PDB: 3is9_A*
3irx_A* 2ze2_A* 3bgr_A* 3qlh_A* 3klf_A* 3qo9_A* 1dlo_A
1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A*
2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* ...
Length = 557
Score = 44.4 bits (105), Expect = 7e-05
Identities = 28/82 (34%), Positives = 42/82 (51%), Gaps = 10/82 (12%)
Query: 187 AELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSN--VSFTNPLVSKVYSCWDLLRSRN 244
EL AIYL L+ + IV+DS+ AL + + LV+++ + L +
Sbjct: 479 TELQAIYLALQ----DSGLEVNIVTDSQYALGIIQAQPDKSESELVNQII---EQLIKKE 531
Query: 245 KVVHFLWCPSHCGIRGNEAVDE 266
KV + W P+H GI GNE VD+
Sbjct: 532 KV-YLAWVPAHKGIGGNEQVDK 552
>1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug
design, transferase; 2.35A {Human immunodeficiency virus
2} SCOP: c.55.3.1 e.8.1.2 PDB: 1mu2_B
Length = 555
Score = 41.3 bits (97), Expect = 6e-04
Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 10/82 (12%)
Query: 187 AELIAIYLCLEAITVHPSDQFLIVSDSRSALAALSN--VSFTNPLVSKVYSCWDLLRSRN 244
AEL A + L + I+ DS+ + +++ + +V+++ + + +
Sbjct: 476 AELEAFAMALT----DSGPKVNIIVDSQYVMGIVASQPTESESKIVNQII---EEMIKKE 528
Query: 245 KVVHFLWCPSHCGIRGNEAVDE 266
+ + W P+H GI GN+ VD
Sbjct: 529 AI-YVAWVPAHKGIGGNQEVDH 549
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 35.2 bits (82), Expect = 0.015
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 238 DLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARN 270
+ L + ++ P H G GNE D AR
Sbjct: 116 ERLTQGMDI-QWMHVPGHSGFIGNEEADRLARE 147
>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase,
hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB:
3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A
Length = 150
Score = 35.2 bits (82), Expect = 0.016
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 238 DLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARN 270
+ L + KV + W P+H GI GNE VD+
Sbjct: 112 EQLIKKEKV-YLAWVPAHKGIGGNEQVDKLVSA 143
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 30.2 bits (69), Expect = 0.96
Identities = 13/47 (27%), Positives = 17/47 (36%), Gaps = 1/47 (2%)
Query: 238 DLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLKLCSPED 284
L + ++V F + H G NE VD AR C P
Sbjct: 113 LLAMAPHRV-RFHFVKGHTGHPENERVDREARRQAQSQAKTPCPPRA 158
>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability,
hydrogen exchange, cooperativity, hydrolase; 1.30A
{Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A
1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A
1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A
3aa5_X 1rbv_A ...
Length = 155
Score = 29.8 bits (68), Expect = 1.0
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 238 DLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARN 270
D ++++ + W H G NE DE AR
Sbjct: 108 DAALGQHQI-KWEWVKGHAGHPENERADELARA 139
>3noy_A 4-hydroxy-3-methylbut-2-EN-1-YL diphosphate synth; iron-sulfur
protein, non-mevalonate pathway, terpene biosynt
isoprenoid biosynthesis; 2.70A {Aquifex aeolicus}
Length = 366
Score = 30.6 bits (70), Expect = 1.2
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 4/38 (10%)
Query: 223 VSFTNPLVSKVYSCWDLLRS---RNKVVHFLWCPSHCG 257
VS T+ V +V + +++L+S R + V + CP+ CG
Sbjct: 242 VSLTDDPVVEVETAYEILKSLGLRRRGVEIVACPT-CG 278
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 29.0 bits (66), Expect = 1.8
Identities = 9/32 (28%), Positives = 12/32 (37%), Gaps = 1/32 (3%)
Query: 238 DLLRSRNKVVHFLWCPSHCGIRGNEAVDEAAR 269
L + ++V F H N DE AR
Sbjct: 109 LKLTTLHRV-TFHKVKGHSDNPYNSRADELAR 139
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 28.6 bits (65), Expect = 3.0
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 238 DLLRSRNKVVHFLWCPSHCGIRGNEAVDEAARNPVNPTQLK 278
D +++ + W H G NE D+ AR +
Sbjct: 110 DKAAQLHQI-DWRWVKGHAGHAENERCDQLARAAAEANPTQ 149
>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 = 28.4 bits (62), Expect = 3.4
Identities = 7/21 (33%), Positives = 10/21 (47%), Gaps = 4/21 (19%)
Query: 275 TQLKLCSPEDFKP---IAASI 292
LKL + D P I A++
Sbjct: 27 ASLKLYAD-DSAPALAIKATM 46
>2xzm_O RPS13E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_O 1ysh_E 3jyv_O* 1s1h_O
Length = 153
Score = 27.6 bits (61), Expect = 5.8
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 95 ISSSDMAPYVRTVPPWSSPSPP--VDLSLGKDRKNDTPS 131
IS S + P+ R P W +P VDLS+ +K TPS
Sbjct: 13 ISGSAL-PFKRRSPKWLHMTPSTVVDLSVKLAKKGLTPS 50
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
0.318 0.133 0.398
Gapped
Lambda K H
0.267 0.0612 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 7,292,219
Number of extensions: 423655
Number of successful extensions: 695
Number of sequences better than 10.0: 1
Number of HSP's gapped: 687
Number of HSP's successfully gapped: 21
Length of query: 491
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 394
Effective length of database: 3,993,456
Effective search space: 1573421664
Effective search space used: 1573421664
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: 59 (26.8 bits)