RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1455
(221 letters)
>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 = 35.6 bits (81), Expect = 0.013
Identities = 23/116 (19%), Positives = 35/116 (30%), Gaps = 20/116 (17%)
Query: 100 YSLITPVDLKAFLKNEFKKKWQIWWDNIQPPNKIKEIKDTVKEWQTSNRNLR-------K 152
Y I V AF+ N K Q D + +EI + + LR K
Sbjct: 18 YKDILSVFEDAFVDNFDCKDVQ---DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSK 74
Query: 153 EEIILSRLRIGHTRLTHGFLMER-----TDPPQCEIRLKYNLNNLQIKDILGDNPR 203
+E ++ + R+ + FLM P + L DN
Sbjct: 75 QEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLY-----NDNQV 125
Score = 34.4 bits (78), Expect = 0.026
Identities = 43/245 (17%), Positives = 85/245 (34%), Gaps = 58/245 (23%)
Query: 4 MWNEVLLRLYKCYVRPIIEYGAPIYGSASEKQLSRLEPIQNMALRIATGAFKS----SRI 59
++N+ +++ Y ++ P + L L P +N+ + G+ K+
Sbjct: 119 LYNDN--QVFAKYNVSRLQ---PY--LKLRQALLELRPAKNVLIDGVLGSGKTWVALDVC 171
Query: 60 ENLQVDAGNNVKIIWIP-SHCGIAGNEEVDKAAQSFTNAQIYSLITPV------------ 106
+ +V + KI W+ +C E V + Q I P
Sbjct: 172 LSYKVQCKMDFKIFWLNLKNCNSP--ETVLEMLQKL-----LYQIDPNWTSRSDHSSNIK 224
Query: 107 ----DLKAFLKNEFKKKWQ----IWWDNIQPPNKIKEIKDTVKEWQTSNRNLRKEEII-- 156
++A L+ K K + N+Q + K T+ R +++
Sbjct: 225 LRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTT----RFKQVTDF 280
Query: 157 LSRLRIGHTRLTH---GFLMERTDPPQCEIRLKYNLNNLQIKD----ILGDNPRTIDLLF 209
LS H L H + + LKY L+ + +D +L NPR + ++
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVK----SLLLKY-LD-CRPQDLPREVLTTNPRRLSIIA 334
Query: 210 KFLKD 214
+ ++D
Sbjct: 335 ESIRD 339
>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 = 33.7 bits (78), Expect = 0.016
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 69 NVKIIWIPSHCGIAGNEEVDKAA 91
V + W+P+H GI GNE+VDK
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLV 141
>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 = 33.5 bits (77), Expect = 0.018
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 69 NVKIIWIPSHCGIAGNEEVDKAAQ 92
+ +H G N+ VD A+
Sbjct: 109 IYSFEKVKAHSGNEFNDYVDMKAK 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 = 33.2 bits (76), Expect = 0.056
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 70 VKIIWIPSHCGIAGNEEVDK 89
V + W+P+H GI GNE+VDK
Sbjct: 533 VYLAWVPAHKGIGGNEQVDK 552
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 31.4 bits (72), Expect = 0.12
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 66 AGNNVKIIWIPSHCGIAGNEEVDKAA 91
G +++ + +P H G GNEE D+ A
Sbjct: 120 QGMDIQWMHVPGHSGFIGNEEADRLA 145
>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 = 30.9 bits (70), Expect = 0.33
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 70 VKIIWIPSHCGIAGNEEVDKAAQS 93
+ + W+P+H GI GN+EVD
Sbjct: 530 IYVAWVPAHKGIGGNQEVDHLVSQ 553
>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 = 29.8 bits (67), Expect = 0.45
Identities = 9/34 (26%), Positives = 12/34 (35%), Gaps = 5/34 (14%)
Query: 63 QVDAGNNVKIIWIPSHCG-----IAGNEEVDKAA 91
+ + II P H GN D+AA
Sbjct: 117 ALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAA 150
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 28.3 bits (64), Expect = 1.3
Identities = 13/50 (26%), Positives = 21/50 (42%)
Query: 62 LQVDAGNNVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPVDLKAF 111
L A + V+ ++ H G NE VD+ A+ +Q + P F
Sbjct: 113 LLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQAKTPCPPRAPTLF 162
>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 = 27.5 bits (62), Expect = 2.2
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 62 LQVDAGNNVKIIWIPSHCGIAGNEEVDKAA 91
+ +K W+ H G NE D+ A
Sbjct: 108 DAALGQHQIKWEWVKGHAGHPENERADELA 137
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 26.7 bits (60), Expect = 3.9
Identities = 6/30 (20%), Positives = 11/30 (36%)
Query: 62 LQVDAGNNVKIIWIPSHCGIAGNEEVDKAA 91
L++ + V + H N D+ A
Sbjct: 109 LKLTTLHRVTFHKVKGHSDNPYNSRADELA 138
>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 = 4.2
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 181 CEIRLKYNLNNLQIKDILGDNPRTIDLL---FKFLKDSNL-LPKL 221
EI + YN+ N Q + + R +D + F+K + + +L
Sbjct: 1841 VEI-VNYNVENQQY--VAAGDLRALDTVTNVLNFIKLQKIDIIEL 1882
Score = 26.9 bits (59), Expect = 5.9
Identities = 6/16 (37%), Positives = 10/16 (62%)
Query: 194 IKDILGDNPRTIDLLF 209
I DI+ +NP + + F
Sbjct: 1661 ILDIVINNPVNLTIHF 1676
>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium
tuberculosis} PDB: 3md0_A* 3nxs_A* 3tk1_A*
Length = 355
Score = 27.1 bits (60), Expect = 5.2
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 8/65 (12%)
Query: 21 IEYGAPIYGSASEKQLSRLEPIQNMALRI----ATGAFKSSRIENL---QVDAGNNVKII 73
+E P + +++ L RL P A R+ G KS+ IE L ++ G+ V ++
Sbjct: 54 VESTRPDHREQAQQLLLRLLPDSGNAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVL 113
Query: 74 WI-PS 77
+ PS
Sbjct: 114 AVDPS 118
>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2,
protein structure initiative, NEW YORK SGX research for
structural genomics; 1.80A {Escherichia coli} SCOP:
c.37.1.10
Length = 341
Score = 27.1 bits (60), Expect = 5.3
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 8/66 (12%)
Query: 20 IIEYGAPIYGSASEKQLSRLEPIQNMALRI----ATGAFKSSRIENL---QVDAGNNVKI 72
++E P + + S + L + P LR+ GA KS+ +E + G V +
Sbjct: 30 LVESRHPRHQALSTQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAV 89
Query: 73 IWI-PS 77
I + PS
Sbjct: 90 IAVDPS 95
>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET:
MSE; 1.70A {Methylobacterium extorquens} SCOP:
c.37.1.10 PDB: 2qm7_A*
Length = 337
Score = 27.0 bits (60), Expect = 5.7
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 20 IIEYGAPIYGSASEKQLSRLEPIQNMALRI----ATGAFKSSRIENL 62
+ E + +A + + P A+R+ G KS+ I+ L
Sbjct: 29 LAESRRADHRAAVRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDAL 75
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 26.3 bits (59), Expect = 6.0
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 62 LQVDAGNNVKIIWIPSHCGIAGNEEVDKAA 91
+ + + W+ H G A NE D+ A
Sbjct: 110 DKAAQLHQIDWRWVKGHAGHAENERCDQLA 139
>2ld4_A Anamorsin; methyltransferase-like fold, alpha/beta fold,
iron-sulfur PR biogenesis, apoptosis; NMR {Homo
sapiens} PDB: 2yui_A
Length = 176
Score = 26.3 bits (57), Expect = 6.4
Identities = 10/34 (29%), Positives = 15/34 (44%)
Query: 56 SSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDK 89
S + + + AG V ++W S A VDK
Sbjct: 2 SFTMADFGISAGQFVAVVWDKSSPVEALKGLVDK 35
>3gd5_A Otcase, ornithine carbamoyltransferase; structural genomics,
NYSGXRC, target 9454P, operon, amino-acid biosynthesis,
ARGI biosynthesis; 2.10A {Gloeobacter violaceus}
Length = 323
Score = 26.4 bits (59), Expect = 8.3
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 24 GAPIYGSASEKQLSRLEPIQNMA 46
G I S S Q+ R EP+++ A
Sbjct: 75 GQVIDLSPSNTQVGRGEPVRDTA 97
>2ef0_A Ornithine carbamoyltransferase; TTHA1199, thermus thermophil
structural genomics, NPPSFA; 2.00A {Thermus
thermophilus}
Length = 301
Score = 26.3 bits (59), Expect = 8.5
Identities = 5/23 (21%), Positives = 12/23 (52%)
Query: 24 GAPIYGSASEKQLSRLEPIQNMA 46
G +Y + + EP++++A
Sbjct: 72 GHAVYLDQKQVGIGEREPVRDVA 94
>2i6u_A Otcase, ornithine carbamoyltransferase; X-RAY crystallography,
ornithine carbamyoltransferase, carbamoyl phosphate, L-
norvaline; 2.20A {Mycobacterium tuberculosis} PDB:
2p2g_A
Length = 307
Score = 26.3 bits (59), Expect = 8.9
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 24 GAPIYGSASEKQLSRLEPIQNMA 46
G + + QL R E +Q+ A
Sbjct: 66 GHAVVVDSGSTQLGRDETLQDTA 88
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
0.320 0.137 0.426
Gapped
Lambda K H
0.267 0.0821 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,455,615
Number of extensions: 197936
Number of successful extensions: 435
Number of sequences better than 10.0: 1
Number of HSP's gapped: 433
Number of HSP's successfully gapped: 37
Length of query: 221
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 131
Effective length of database: 4,188,903
Effective search space: 548746293
Effective search space used: 548746293
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (24.8 bits)