RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10817
(199 letters)
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 33.3 bits (77), Expect = 0.019
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 25 LDLVACGKEISFMWCPSHCGISGNEAVDVAAKN 57
L+ + G +I +M P H G GNE D A+
Sbjct: 115 LERLTQGMDIQWMHVPGHSGFIGNEEADRLARE 147
>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 = 32.7 bits (75), Expect = 0.028
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 32 KEISFMWCPSHCGISGNEAVDVAAK 56
SF +H G N+ VD+ AK
Sbjct: 108 GIYSFEKVKAHSGNEFNDYVDMKAK 132
>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 = 32.1 bits (73), Expect = 0.066
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 5/37 (13%)
Query: 25 LDLVACGKEISFMWCPSHCG-----ISGNEAVDVAAK 56
L + K +S + CP H GN D AA+
Sbjct: 115 LKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAR 151
>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 = 31.0 bits (71), Expect = 0.11
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 25 LDLVACGKEISFMWCPSHCGISGNEAVDVAAKN 57
++ + +++ W P+H GI GNE VD
Sbjct: 111 IEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA 143
>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 = 30.9 bits (70), Expect = 0.23
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 31 GKE-ISFMWCPSHCGISGNEAVD 52
KE + W P+H GI GNE VD
Sbjct: 529 KKEKVYLAWVPAHKGIGGNEQVD 551
>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 = 30.0 bits (67), Expect = 0.62
Identities = 27/169 (15%), Positives = 59/169 (34%), Gaps = 46/169 (27%)
Query: 71 SDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKP---NIEKWPSSNRKTRLEEVVLTRMR- 126
Y L+ +++ + ++ + + + NI +W N ++ L +
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEW-LENPSNTPDKDYLLSIPI 236
Query: 127 ----IGHTRLTHSYLFSR----SPQP--------TCRCGDILT----------------V 154
IG +L H + ++ +P T ++T V
Sbjct: 237 SCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSV 296
Query: 155 KHILTCPLDIQLRS--SLPN---PPSLTDETT----GVDALMSLLKSLN 194
+ +T I +R + PN PPS+ +++ GV + M + +L
Sbjct: 297 RKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLT 345
Score = 28.9 bits (64), Expect = 1.4
Identities = 23/138 (16%), Positives = 39/138 (28%), Gaps = 51/138 (36%)
Query: 21 YSTWLDLVACGKEISF---------------MWCPSHCGISGNEAVDVAAKNPSPSFPPL 65
Y+ L + +S + P G + A NP
Sbjct: 1767 YAA---LASLADVMSIESLVEVVFYRGMTMQVAVPR--DELGRSNYGMIAINPGR---VA 1818
Query: 66 KLCSASDYKPLIKKI-------VQ------RNWQ----------SSWNSVPNGNKLKSIK 102
S + +++++ V+ N Q + +V N KL+ I
Sbjct: 1819 ASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKID 1878
Query: 103 PNIEKWPSSNRKTRLEEV 120
I + S LEEV
Sbjct: 1879 --IIELQKS---LSLEEV 1891
Score = 28.1 bits (62), Expect = 2.4
Identities = 16/87 (18%), Positives = 21/87 (24%), Gaps = 44/87 (50%)
Query: 152 LTVKH-ILTCPLDI---------QLR----SSLPNPPSLTDETTGVDALMS--------- 188
LT+ H L L + QL+ LP P T+ D +
Sbjct: 9 LTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEP---TEGFAADDEPTTPAELVGKFL 65
Query: 189 ------------------LLKSLNIFE 197
L L FE
Sbjct: 66 GYVSSLVEPSKVGQFDQVLNLCLTEFE 92
Score = 27.3 bits (60), Expect = 4.6
Identities = 4/21 (19%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 179 ETTGVDALMSLLKSLNIFEKI 199
+ +D + ++L + + +KI
Sbjct: 1858 DLRALDTVTNVLNFIKL-QKI 1877
>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 = 29.3 bits (66), Expect = 0.79
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 31 GKEISFM-WCPSHCGISGNEAVD 52
KE ++ W P+H GI GN+ VD
Sbjct: 526 KKEAIYVAWVPAHKGIGGNQEVD 548
>2hr0_A Complement C3 beta chain; complement component C3B, immune system;
HET: THC; 2.26A {Homo sapiens} PDB: 2i07_A* 2wii_A*
2win_A* 2xwj_A* 3l3o_A* 3l5n_A* 3nms_A* 3nsa_A* 3ohx_A*
3t4a_A 2a74_A* 2a73_A* 2qki_A* 3g6j_A 2ice_A* 2icf_A*
2xwb_A*
Length = 645
Score = 29.3 bits (64), Expect = 0.87
Identities = 21/139 (15%), Positives = 39/139 (28%), Gaps = 24/139 (17%)
Query: 34 ISFMWCPSHCGISGNEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSVP 93
I F P + + V NP D P + V + + S+
Sbjct: 333 IHFTKTPKYFKPGMPFDLMVFVTNP-------------DGSPAYRVPVAVQGEDTVQSLT 379
Query: 94 NGNKLKSIKPNIEKWPSS-NRKTRLEEVVLTRMRIGHTRLTH----------SYLFSRSP 142
G+ + + N + R ++ L+ + +YL
Sbjct: 380 QGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQALPYSTVGNSNNYLHLSVL 439
Query: 143 QPTCRCGDILTVKHILTCP 161
+ R G+ L V +L
Sbjct: 440 RTELRPGETLNVNFLLRMD 458
>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 = 28.2 bits (64), Expect = 1.2
Identities = 14/42 (33%), Positives = 17/42 (40%), Gaps = 6/42 (14%)
Query: 24 W--LDLVACGKEISFMWCPSHCGISGNEAVDV----AAKNPS 59
W LD +I + W H G NE D AA NP+
Sbjct: 104 WQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPT 145
>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 = 28.7 bits (63), Expect = 1.7
Identities = 25/153 (16%), Positives = 50/153 (32%), Gaps = 26/153 (16%)
Query: 65 LKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEK---WPSSNRKTRLEEVV 121
+ L YK K +++ W ++ N N +++ ++K N +R +
Sbjct: 166 VALDVCLSYKVQCK----MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSS 221
Query: 122 LTRMRIGHTRLTHSYLFSRSPQPTCRCGDIL----TVKHI----LTCPL-----DIQLRS 168
++RI + L P C +L K L+C + Q+
Sbjct: 222 NIKLRIHSIQAELRRLLKSKPYE--NCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTD 279
Query: 169 SLPNPPSLTDETTGVDALMSLLK--SLNIFEKI 199
L + T + M+L ++ K
Sbjct: 280 FL--SAATTTHISLDHHSMTLTPDEVKSLLLKY 310
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 27.1 bits (61), Expect = 2.5
Identities = 8/42 (19%), Positives = 12/42 (28%), Gaps = 6/42 (14%)
Query: 24 W--LDLVACGKEISFMWCPSHCGISGNEAVDV----AAKNPS 59
W + + ++F H N D A K S
Sbjct: 105 WQEILKLTTLHRVTFHKVKGHSDNPYNSRADELARLAIKENS 146
>2h6o_A Major outer envelope glycoprotein GP350; viral protein; HET: NAG
MAN BMA NDG GAL FUC; 3.50A {Human herpesvirus 4}
Length = 470
Score = 27.6 bits (60), Expect = 2.9
Identities = 15/71 (21%), Positives = 27/71 (38%), Gaps = 5/71 (7%)
Query: 111 SNRKTRLEEVVLTRMRIGHTRLTHSYLFSRSPQPTCRCGDILTVKHILTCPLDIQLRSSL 170
S T + +++TR T TH +FS++P+ T + T + L
Sbjct: 394 SGLGTAPKTLIITRTATNATTTTHKVIFSKAPESTTTSPTLNTTGFA-----APNTTTGL 448
Query: 171 PNPPSLTDETT 181
P+ + T
Sbjct: 449 PSSTHVPTNLT 459
>2pgs_A Putative deoxyguanosinetriphosphate triphosphohyd;
deoxyguanosinetriphosphate triphsphohydrolase,
pseudomonas S PV. phaseolicola 1448A; 2.35A {Pseudomonas
syringae PV}
Length = 451
Score = 27.3 bits (61), Expect = 3.7
Identities = 7/7 (100%), Positives = 7/7 (100%)
Query: 129 HTRLTHS 135
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 = 27.4 bits (61), Expect = 3.8
Identities = 7/7 (100%), Positives = 7/7 (100%)
Query: 129 HTRLTHS 135
HTRLTHS
Sbjct: 63 HTRLTHS 69
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 26.8 bits (60), Expect = 4.1
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 6/47 (12%)
Query: 24 W--LDLVACGKEISFMWCPSHCGISGNEAVDV----AAKNPSPSFPP 64
W L L + F + H G NE VD A++ + + P
Sbjct: 109 WEALLLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQAKTPCP 155
>1l9v_A Rotavirus-NSP2; alpha/beta protein, HIT-like fold, octamer, two
domain prote protein; 2.60A {Simian 11 rotavirus} SCOP:
d.13.2.1 d.216.1.1 PDB: 2r7c_A* 2r7j_A 2r7p_A* 2r8f_A*
Length = 317
Score = 26.7 bits (58), Expect = 5.2
Identities = 14/63 (22%), Positives = 30/63 (47%), Gaps = 8/63 (12%)
Query: 66 KLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKL--------KSIKPNIEKWPSSNRKTRL 117
K +D+ L ++I+ +NW + +S+ GN L + +KP + + ++
Sbjct: 250 KTGVNNDFNLLDQRIIWQNWYAFTSSMKQGNTLDVCKRLLFQKMKPEKNPFKGLSTDRKM 309
Query: 118 EEV 120
+EV
Sbjct: 310 DEV 312
>2z1d_A Hydrogenase expression/formation protein HYPD; [NIFE] hydrogenase
maturation, [4Fe-4S] cluster, thiol redox binding
protein; HET: CSW; 2.07A {Thermococcus kodakarensis}
Length = 372
Score = 26.2 bits (58), Expect = 8.3
Identities = 8/20 (40%), Positives = 10/20 (50%), Gaps = 1/20 (5%)
Query: 144 PTCRCGDILT-VKHILTCPL 162
CRCG +L + CPL
Sbjct: 321 KGCRCGAVLRGLALPTDCPL 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 0.131 0.407
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: 2,953,832
Number of extensions: 159932
Number of successful extensions: 266
Number of sequences better than 10.0: 1
Number of HSP's gapped: 266
Number of HSP's successfully gapped: 24
Length of query: 199
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 110
Effective length of database: 4,216,824
Effective search space: 463850640
Effective search space used: 463850640
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: 55 (24.8 bits)