RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15899
(104 letters)
>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 = 45.9 bits (109), Expect = 3e-07
Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 11/87 (12%)
Query: 5 SNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAI-ANPYLS-CPIISQIYSAWCDL 62
+N EL AI L L+ + +V+DS +L I A P S +++QI
Sbjct: 475 TNQKTELQAIYLALQ----DSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIE----- 525
Query: 63 KTVGQYYVKLMWCPSHCGIRGNEAVDQ 89
+ + + V L W P+H GI GNE VD+
Sbjct: 526 QLIKKEKVYLAWVPAHKGIGGNEQVDK 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 = 42.8 bits (101), Expect = 3e-06
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 11/87 (12%)
Query: 5 SNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAI-ANPYLS-CPIISQIYSAWCDL 62
+N AEL A + L P + ++ DS + + + P S I++QI
Sbjct: 472 TNQQAELEAFAMALTDSG--PKVN--IIVDSQYVMGIVASQPTESESKIVNQIIE----- 522
Query: 63 KTVGQYYVKLMWCPSHCGIRGNEAVDQ 89
+ + + + + W P+H GI GN+ VD
Sbjct: 523 EMIKKEAIYVAWVPAHKGIGGNQEVDH 549
>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 = 41.4 bits (97), Expect = 7e-06
Identities = 23/108 (21%), Positives = 41/108 (37%), Gaps = 26/108 (24%)
Query: 9 AELIAILLCLRSIKNHPAMRFLLVSDSM---------GSLSAIANPYLSCPIISQIYSAW 59
AELIA+ L+ + + +DS I N I++ + + +
Sbjct: 66 AELIALTQALKMAEGKK---LNVYTDSRYAFATAHVHSEGREIKNKNE---ILALLKALF 119
Query: 60 CDLKTVGQYYVKLMWCPSHCG-----IRGNEAVDQAAKDPLLSPVIEK 102
+ + ++ CP H RGN DQAA++ + V+E
Sbjct: 120 LPKR------LSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLET 161
>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 = 38.5 bits (90), Expect = 7e-05
Identities = 16/93 (17%), Positives = 28/93 (30%), Gaps = 14/93 (15%)
Query: 6 NGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAI-----ANPYLSCPIISQIYSAWC 60
N E+ A L ++ ++ ++ D G A + A+
Sbjct: 50 NVAGEIAAALYAVKKASQLG-VKIRILHDYAGIAFWATGEWKAKNEFT--------QAYA 100
Query: 61 DLKTVGQYYVKLMWCPSHCGIRGNEAVDQAAKD 93
L + +H G N+ VD AK
Sbjct: 101 KLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKS 133
>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 = 32.5 bits (75), Expect = 0.011
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 70 VKLMWCPSHCGIRGNEAVDQAAK 92
V L W P+H GI GNE VD+
Sbjct: 120 VYLAWVPAHKGIGGNEQVDKLVS 142
>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 = 0.026
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 70 VKLMWCPSHCGIRGNEAVDQAAKD 93
++ M P H G GNE D+ A++
Sbjct: 124 IQWMHVPGHSGFIGNEEADRLARE 147
>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal
domain, fusion protein, maltose binding protein, HYDR;
HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}
Length = 141
Score = 30.0 bits (68), Expect = 0.085
Identities = 7/35 (20%), Positives = 13/35 (37%)
Query: 2 FHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSM 36
+N +AE ++ L A ++ DS
Sbjct: 42 GRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSK 76
>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 = 0.35
Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 21/77 (27%)
Query: 8 IAELI--AILLCLRSIKNHPAMRFLLVSDSMGSLSAIANP-------YL-----SCPII- 52
+ +LI + I+ + + + L + NP YL SCP+I
Sbjct: 184 VGDLIKFSAETLSELIRTTLDAEKVF-TQGLNILEWLENPSNTPDKDYLLSIPISCPLIG 242
Query: 53 -SQI--YSAWCDLKTVG 66
Q+ Y K +G
Sbjct: 243 VIQLAHYVVTA--KLLG 257
Score = 27.7 bits (61), Expect = 0.70
Identities = 11/92 (11%), Positives = 33/92 (35%), Gaps = 10/92 (10%)
Query: 6 NGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCDLKTV 65
G+ +L ++ + + P + + + + ++ I++ S W
Sbjct: 241 IGVIQLAHYVVTAKLLGFTPGE----LRSYLKGATGHSQGLVTAVAIAETDS-WESFFVS 295
Query: 66 GQYYVKLM-WCPSHCGIRGNEAVDQAAKDPLL 96
+ + ++ + G+R EA + P +
Sbjct: 296 VRKAITVLFFI----GVRCYEAYPNTSLPPSI 323
>3a32_A Probable threonyl-tRNA synthetase 1; aeropyrum pernix K1, protein
biosynthesis, aminoacyl-tRNA synthetase, ATP-binding,
cytoplasm, ligase; 2.30A {Aeropyrum pernix} PDB: 3a31_A
Length = 471
Score = 26.1 bits (58), Expect = 2.1
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 67 QYYVKLMWCPSHCGI 81
++ VK M CP H +
Sbjct: 104 EFAVKPMNCPYHILL 118
>2job_A Antilipopolysaccharide factor; ALF, lipid A binding protein,
endotoxin, lipid binding protein; NMR {Penaeus monodon}
Length = 102
Score = 25.5 bits (55), Expect = 2.2
Identities = 12/33 (36%), Positives = 13/33 (39%), Gaps = 7/33 (21%)
Query: 68 YYVKLMWCPSHCGIRGN-------EAVDQAAKD 93
YY MWCP IRG + AKD
Sbjct: 48 YYKGRMWCPGWTAIRGEASTRSQSGVAGKTAKD 80
>1ygr_A CD45 protein tyrosine phosphatase; protein tyrosine phosphatase,
RPTP, LCA, lymphocyte activation, hydrolase; HET: PTR;
2.90A {Homo sapiens} PDB: 1ygu_A*
Length = 610
Score = 25.9 bits (57), Expect = 2.8
Identities = 7/25 (28%), Positives = 11/25 (44%), Gaps = 3/25 (12%)
Query: 3 HCSNGIAE---LIAILLCLRSIKNH 24
HC +G + A+L L S +
Sbjct: 545 HCRDGSQQTGIFCALLNLLESAETE 569
>3k9t_A Putative peptidase; structural genomics, joint center for ST
genomics, JCSG, protein structure initiative, PSI-2,
aminop hydrolase; 2.37A {Clostridium acetobutylicum}
Length = 435
Score = 26.1 bits (56), Expect = 2.8
Identities = 13/59 (22%), Positives = 25/59 (42%)
Query: 3 HCSNGIAELIAILLCLRSIKNHPAMRFLLVSDSMGSLSAIANPYLSCPIISQIYSAWCD 61
+G+A + I L +K + RFL +++GS++ ++ I A C
Sbjct: 196 DNLSGVALITFIAKALSKLKTKYSYRFLFAPETIGSITWLSRNEDKLKNIKMGLVATCV 254
>1su1_A Hypothetical protein YFCE; structural genomics, phosphoesterase,
PSI, protein structure initiative, midwest center for
structural genomics, MCSG; 2.25A {Escherichia coli}
SCOP: d.159.1.7
Length = 208
Score = 25.5 bits (56), Expect = 3.1
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 22 KNHPAMRFLLVSDSMGSLSAI 42
+++ M+ + SD GSL A
Sbjct: 21 QSNAMMKLMFASDIHGSLPAT 41
>1lar_A Protein (LAR); tyrosine phosphatease, LAR protein, hydrolase; 2.00A
{Homo sapiens} SCOP: c.45.1.2 c.45.1.2 PDB: 2fh7_A
2nv5_A
Length = 575
Score = 25.8 bits (57), Expect = 3.7
Identities = 6/25 (24%), Positives = 11/25 (44%), Gaps = 3/25 (12%)
Query: 3 HCSNGIAE---LIAILLCLRSIKNH 24
HCS G+ I + + L ++
Sbjct: 506 HCSAGVGRTGVFITLSIVLERMRYE 530
>2jjd_A Receptor-type tyrosine-protein phosphatase epsilo; transmembrane,
phosphoprotein, consorti structural, glycoprotein, SGC,
PTPRE, membrane genomics; 3.20A {Homo sapiens}
Length = 599
Score = 25.4 bits (56), Expect = 4.0
Identities = 8/25 (32%), Positives = 10/25 (40%), Gaps = 3/25 (12%)
Query: 3 HCSNGIAE---LIAILLCLRSIKNH 24
HCS G IA+ L +K
Sbjct: 524 HCSAGAGRTGTFIALSNILERVKAE 548
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 25.6 bits (56), Expect = 4.4
Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 16/64 (25%)
Query: 50 PIISQIYSAWCDLKT---------VGQYYVKLMWCPSHCGIRGNEA----VDQAAKDPLL 96
+ + Y+ W D KT +Y ++ H GIR E K ++
Sbjct: 867 NLKGRPYTGWVDSKTKEPVDDKDVKAKYETSIL---EHSGIRLIEPELFNGYNPEKKEMI 923
Query: 97 SPVI 100
VI
Sbjct: 924 QEVI 927
>2nlk_A Protein tyrosine phosphatase, receptor type, G VA (fragment);
PTPRG, R-PTP gamma, protein tyrosine phosphatase gamma,
D3S1 HPTPG, RPTPG, PTPG; 2.40A {Homo sapiens}
Length = 627
Score = 25.5 bits (56), Expect = 4.5
Identities = 5/25 (20%), Positives = 9/25 (36%), Gaps = 3/25 (12%)
Query: 3 HCSNGIAE---LIAILLCLRSIKNH 24
H G L A+ + ++N
Sbjct: 525 HDEYGAVSAGMLCALTTLSQQLENE 549
>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 = 24.8 bits (55), Expect = 5.5
Identities = 11/31 (35%), Positives = 14/31 (45%), Gaps = 4/31 (12%)
Query: 70 VKLMWCPSHCGIRGNEAVDQ----AAKDPLL 96
+K W H G NE D+ AA +P L
Sbjct: 116 IKWEWVKGHAGHPENERADELARAAAMNPTL 146
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded
RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus
tokodaii} PDB: 3aly_A
Length = 149
Score = 24.6 bits (54), Expect = 5.6
Identities = 5/34 (14%), Positives = 15/34 (44%)
Query: 2 FHCSNGIAELIAILLCLRSIKNHPAMRFLLVSDS 35
+ +N +AE ++ + ++ ++ DS
Sbjct: 44 INSTNNVAEYSGLICLMETMLRLGISSPIIKGDS 77
>1r8n_A STI, kunitz trypsin inhibitor; kunitz-type trypsin/kallikrein
inhibitor, beta-trefoil fold, flamboyant, hydrolase
inhibitor; 1.75A {Delonix regia} SCOP: b.42.4.1
Length = 185
Score = 24.6 bits (53), Expect = 6.0
Identities = 5/28 (17%), Positives = 13/28 (46%)
Query: 53 SQIYSAWCDLKTVGQYYVKLMWCPSHCG 80
++ + ++ +G KL++CP
Sbjct: 117 GELVRGFFKIEKLGSLAYKLVFCPKSDS 144
>2qn4_A RASI, alpha-amylase/subtilisin inhibitor; amylase inhibitor, alpha-
amylase inhibitor, protease inhibitor, serine protease
inhibitor; 1.80A {Oryza sativa subsp}
Length = 200
Score = 24.7 bits (53), Expect = 7.9
Identities = 7/31 (22%), Positives = 10/31 (32%), Gaps = 1/31 (3%)
Query: 53 SQIYSAWCDLKTVGQYYVKLMWCPSHCGIRG 83
++ G Y KL+ C C G
Sbjct: 141 PSGRENAFRVEKYGGGY-KLVSCRDSCQDLG 170
>1nyr_A Threonyl-tRNA synthetase 1; ATP, threonine, ligase; HET: ATP; 2.80A
{Staphylococcus aureus} SCOP: c.51.1.1 d.15.10.1
d.67.1.1 d.104.1.1 PDB: 1nyq_A*
Length = 645
Score = 24.4 bits (54), Expect = 9.3
Identities = 5/15 (33%), Positives = 7/15 (46%)
Query: 67 QYYVKLMWCPSHCGI 81
++ M CP H I
Sbjct: 328 SMVLRPMNCPHHMMI 342
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
0.325 0.137 0.441
Gapped
Lambda K H
0.267 0.0550 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,569,407
Number of extensions: 75523
Number of successful extensions: 225
Number of sequences better than 10.0: 1
Number of HSP's gapped: 223
Number of HSP's successfully gapped: 40
Length of query: 104
Length of database: 6,701,793
Length adjustment: 69
Effective length of query: 35
Effective length of database: 4,775,244
Effective search space: 167133540
Effective search space used: 167133540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.8 bits)