RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15839
(293 letters)
>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 = 43.9 bits (104), Expect = 8e-06
Identities = 12/90 (13%), Positives = 24/90 (26%), Gaps = 7/90 (7%)
Query: 87 NNINSIFTAELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKN--TSIPLIAHILNT 144
E+ A ++ + V I+ D + A
Sbjct: 45 AATMRNVAGEIAAALYAVKKASQLG-VKIRILHDYAG-IAFWATGEWKAKNEFTQAYAKL 102
Query: 145 WHTLKSCGKKVAFLWCPSHTGISGNEIVDR 174
+ + +F +H+G N+ VD
Sbjct: 103 MNQYR---GIYSFEKVKAHSGNEFNDYVDM 129
>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-05
Identities = 22/91 (24%), Positives = 38/91 (41%), Gaps = 11/91 (12%)
Query: 95 AELLALVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTSIPLIAHILNTWHTLKSCGKK 154
AEL+AL L + +N + DS A + A+ ++ I + LK+
Sbjct: 66 AELIALTQALKMAE-GKKLN--VYTDSRYAF-ATAHVHSEGREIKNKNEILALLKALFLP 121
Query: 155 --VAFLWCPSHTG-----ISGNEIVDRATRQ 178
++ + CP H GN + D+A R+
Sbjct: 122 KRLSIIHCPGHQKGNSAEARGNRMADQAARE 152
>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 = 41.3 bits (97), Expect = 3e-04
Identities = 29/84 (34%), Positives = 40/84 (47%), Gaps = 14/84 (16%)
Query: 95 AELLALVFCL-DSVKNRPDVNTLIVCDSMSALTSIANK--NTSIPLIAHILNTWHTLKSC 151
EL A+ L DS +VN IV DS AL I + + L+ I+ +
Sbjct: 479 TELQAIYLALQDS---GLEVN--IVTDSQYALGIIQAQPDKSESELVNQIIE-----QLI 528
Query: 152 GKKVAFL-WCPSHTGISGNEIVDR 174
K+ +L W P+H GI GNE VD+
Sbjct: 529 KKEKVYLAWVPAHKGIGGNEQVDK 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 = 39.3 bits (92), Expect = 0.001
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 14/84 (16%)
Query: 95 AELLALVFCL-DSVKNRPDVNTLIVCDSMSALTSIANK--NTSIPLIAHILNTWHTLKSC 151
AEL A L DS P VN I+ DS + +A++ + ++ I+ +
Sbjct: 476 AELEAFAMALTDS---GPKVN--IIVDSQYVMGIVASQPTESESKIVNQIIE-----EMI 525
Query: 152 GKKVAFL-WCPSHTGISGNEIVDR 174
K+ ++ W P+H GI GN+ VD
Sbjct: 526 KKEAIYVAWVPAHKGIGGNQEVDH 549
>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 = 37.5 bits (86), Expect = 0.005
Identities = 32/159 (20%), Positives = 60/159 (37%), Gaps = 38/159 (23%)
Query: 1 MHKILFGNVDSFNIT----PNKPLPLKIR---FNCIREVSAVLKNTKVVPYSQGFPPWYS 53
+H+ + VD +NI + +P + ++ I LKN + F +
Sbjct: 445 LHRSI---VDHYNIPKTFDSDDLIPPYLDQYFYSHI---GHHLKNIEHPERMTLFRMVFL 498
Query: 54 DFPVVDLSLYGSKTIQNTSCAVYAGGSA----------KSYILNNINSIFTAELLALVFC 103
DF ++ + I++ S A A GS K YI +N + + A+
Sbjct: 499 DFRFLE------QKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDP-KYERLVNAI--- 548
Query: 104 LDSVKNRPDVNTLIVCDSMSALTSIA--NKNTSIPLIAH 140
+ P + ++C + L IA ++ +I AH
Sbjct: 549 ---LDFLPKIEENLICSKYTDLLRIALMAEDEAIFEEAH 584
>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 = 36.2 bits (83), Expect = 0.012
Identities = 47/265 (17%), Positives = 77/265 (29%), Gaps = 89/265 (33%)
Query: 13 NITPNKPLPLKIRFNC-----IRE-VSAVLKNTKVVPYSQGFPPWYSDFPVVDLSL---- 62
+I N P+ L I F IRE SA++ T G F ++
Sbjct: 1663 DIVINNPVNLTIHFGGEKGKRIRENYSAMIFET----IVDGKLKTEKIFKEINEHSTSYT 1718
Query: 63 -YGSK-----TIQNTSCAVYAGGSAKSYILNNINSIFTAELLALVFCLDSVKNRPDVNTL 116
K T Q T A + E A L K++ L
Sbjct: 1719 FRSEKGLLSAT-QFTQPA-----------------LTLMEK-AAFEDL---KSK----GL 1752
Query: 117 IVCDSM---------SALTSIANKNTSIPL-------------IAHILNTWHTLKSCGKK 154
I D+ +AL S+A+ + + + + +S
Sbjct: 1753 IPADATFAGHSLGEYAALASLAD---VMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGM 1809
Query: 155 VAFLWCPSHTGISGNE-----IVDRATRQLDG-AEFVNLSSPADLISV-GKKYIHEKWQK 207
+A P S ++ +V+R ++ E VN + G +
Sbjct: 1810 IAIN--PGRVAASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDL-------R 1860
Query: 208 SWSDLTN--NKLKCVKPTIGPWNVS 230
+ +TN N +K K I S
Sbjct: 1861 ALDTVTNVLNFIKLQKIDIIELQKS 1885
>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 = 31.4 bits (72), Expect = 0.15
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 154 KVAFLWCPSHTGISGNEIVDRATRQ 178
KV W P+H GI GNE VD+
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSA 143
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 29.8 bits (68), Expect = 0.49
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 154 KVAFLWCPSHTGISGNEIVDRATRQLDGAE 183
+ ++ P H+G GNE DR R+ GA+
Sbjct: 123 DIQWMHVPGHSGFIGNEEADRLARE--GAK 150
>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 = 28.8 bits (63), Expect = 1.4
Identities = 7/22 (31%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 66 KTIQNTSCAVYAGGSAKSYILN 87
K +Q S +YA SA + +
Sbjct: 23 KKLQA-SLKLYADDSAPALAIK 43
>2ob5_A AGR_C_3656P, hypothetical protein ATU2016; putavite sugar binding
protein, S genomics, PSI-2, protein structure
initiative; HET: MSE; 1.60A {Agrobacterium tumefaciens
str} SCOP: c.133.1.1
Length = 153
Score = 27.4 bits (60), Expect = 3.9
Identities = 20/130 (15%), Positives = 45/130 (34%), Gaps = 17/130 (13%)
Query: 82 KSYILNNINSIFTAELLALV---------------FCLDSVKNRPDVNTLIVCDSMSALT 126
+L NI+ A++L + F DSV + V ++ D++SA
Sbjct: 2 FQGMLKNIDPALNADVLHALRAMGHGDTLVISDTNFPSDSVARQTTVGKVLHIDNVSAAR 61
Query: 127 SIANKNTSIPLIAHILNTWHTLKSCG--KKVAFLWCPSHTGISGNEIVDRATRQLDGAEF 184
++ + +PL + + ++ G ++ + I E ++ F
Sbjct: 62 AMKAILSVLPLDTPLQPSVGRMEVMGAPDQLEPVQVEVQQEIDAAEGKSAPMYGIERFAF 121
Query: 185 VNLSSPADLI 194
+ A +
Sbjct: 122 YEKAKQAYCV 131
>2yuh_A Tubulin-specific chaperone C; microtubule, beta-tubulin folding,
beta-roll, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 179
Score = 27.4 bits (60), Expect = 5.1
Identities = 10/41 (24%), Positives = 17/41 (41%)
Query: 222 PTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDP 262
P + DC++ V ++RI T+ T +L S
Sbjct: 66 PVSTSVFLEDCSDCVLAVACQQLRIHSTKDTRIFLQVTSRA 106
>3bh7_B Protein XRP2; protein-protein complex, GTPase activating protein
and GTPase, retinitis pigmentosa, GTP-binding,
lipoprotein, myristate; HET: GDP; 1.90A {Homo sapiens}
PDB: 3bh6_B* 2bx6_A
Length = 352
Score = 27.5 bits (60), Expect = 6.2
Identities = 7/41 (17%), Positives = 14/41 (34%)
Query: 222 PTIGPWNVSDCNNRYEEVVLTRVRIGHTRLTHSYLFTRSDP 262
P G +C + + + R+ R +L + P
Sbjct: 97 PVKGSVFFRNCRDCKCTLACQQFRVRDCRKLEVFLCCATQP 137
>2pgs_A Putative deoxyguanosinetriphosphate triphosphohyd;
deoxyguanosinetriphosphate triphsphohydrolase,
pseudomonas S PV. phaseolicola 1448A; 2.35A {Pseudomonas
syringae PV}
Length = 451
Score = 27.0 bits (60), Expect = 7.8
Identities = 7/7 (100%), Positives = 7/7 (100%)
Query: 248 HTRLTHS 254
HTRLTHS
Sbjct: 61 HTRLTHS 67
>3bg2_A DGTP triphosphohydrolase; structural genomics, NYSGXRC, target
10395N, triphosphohydro PSI-2, protein structure
initiative; 1.95A {Leeuwenhoekiella blandensis}
Length = 444
Score = 27.0 bits (60), Expect = 8.0
Identities = 7/7 (100%), Positives = 7/7 (100%)
Query: 248 HTRLTHS 254
HTRLTHS
Sbjct: 63 HTRLTHS 69
>2eqa_A Hypothetical protein ST1526; YRDC/RIBB fold, YRDC domain, SUA5
domain, structural genomics, NPPSFA; HET: AMP; 1.80A
{Sulfolobus tokodaii} PDB: 3aje_A* 4e1b_A*
Length = 352
Score = 26.8 bits (60), Expect = 9.3
Identities = 12/38 (31%), Positives = 15/38 (39%), Gaps = 4/38 (10%)
Query: 106 SVKNRPDVNTLIV-CDSMSALTSIANKNTSIPLIAHIL 142
KNRP N LIV + L +A IP +
Sbjct: 55 QAKNRPVDNPLIVHIADFNQLFEVA---KDIPDKVLEI 89
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 0.132 0.402
Gapped
Lambda K H
0.267 0.0802 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,221,011
Number of extensions: 230272
Number of successful extensions: 532
Number of sequences better than 10.0: 1
Number of HSP's gapped: 528
Number of HSP's successfully gapped: 19
Length of query: 293
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 200
Effective length of database: 4,105,140
Effective search space: 821028000
Effective search space used: 821028000
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 (25.6 bits)