RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9737
(368 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 = 38.5 bits (90), Expect = 8e-04
Identities = 11/50 (22%), Positives = 18/50 (36%)
Query: 158 NPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEPITNH 207
N + + + + + F +H G ND D +AK A H
Sbjct: 93 NEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSALGIRDLEH 142
>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 = 37.1 bits (85), Expect = 0.010
Identities = 26/154 (16%), Positives = 51/154 (33%), Gaps = 32/154 (20%)
Query: 226 W------NTTWSNINPSENKLRRIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHL 279
W N+ + + + L +I + +R D +++RI + L
Sbjct: 186 WLNLKNCNSPETVLEMLQKLLYQI--------DPNWTSRSDHSSNIKLRIHSIQAELRRL 237
Query: 280 FKREERPIC----DSCHEPLTVEHIILHCNKL---RFRPPSFLEESTQDILSDQYGQLDT 332
K + C + L C L RF+ D LS +
Sbjct: 238 LKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK-------QVTDFLSAATTTHIS 290
Query: 333 VNNLNDSLTDR----LCNRYSTVHKKEESREMIT 362
+++ + +LT L +Y ++ RE++T
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT 324
Score = 27.5 bits (60), Expect = 8.9
Identities = 19/139 (13%), Positives = 41/139 (29%), Gaps = 42/139 (30%)
Query: 267 MRIGHTKITHSHL--FKR--EERPICDSCHEPLT---VEHIILHCNK----------LRF 309
+ + I F + + + D L+ ++HII+ + L
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLS 73
Query: 310 RPPSFLEESTQDILSDQYG----------------------QLDTVNNLNDSLTDRLCNR 347
+ +++ +++L Y Q D + N N +R
Sbjct: 74 KQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSR 133
Query: 348 YSTVHK-KEESREMITRPH 365
K ++ E+ RP
Sbjct: 134 LQPYLKLRQALLEL--RPA 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 = 34.9 bits (79), Expect = 0.013
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 13/41 (31%)
Query: 162 KEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSE 202
+ +++ + S K L+ D A A A KAT E
Sbjct: 20 QALKKLQA----SLK-LYAD--------DSAPALAIKATME 47
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 31.0 bits (71), Expect = 0.27
Identities = 9/44 (20%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 160 LVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEP 203
++ + I + P H G GN++AD A++ +
Sbjct: 111 DFVALERLTQGMDIQWM--HVPGHSGFIGNEEADRLAREGAKQS 152
>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 = 0.27
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 160 LVKE-IQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA 199
LV + I++ ++ W P+H GI GN+Q D
Sbjct: 106 LVNQIIEQLIKKEKVYLA--WVPAHKGIGGNEQVDKLVSAG 144
>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 = 32.0 bits (73), Expect = 0.29
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 158 NPLVKEI-QERSSNSQISFKFLWCPSHVGISGNDQAD 193
+ LV +I ++ ++ W P+H GI GN+Q D
Sbjct: 517 SELVNQIIEQLIKKEKVYLA--WVPAHKGIGGNEQVD 551
>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 = 31.0 bits (70), Expect = 0.34
Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 7/62 (11%)
Query: 157 PNPLVKEIQE--RSSNSQISFKFLWCPSHVG-----ISGNDQADAEAKKATSEPITNHSL 209
EI ++ + CP H GN AD A++A + + S
Sbjct: 104 EIKNKNEILALLKALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLETST 163
Query: 210 LL 211
LL
Sbjct: 164 LL 165
>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 = 0.69
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 158 NPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQAD 193
+ +V +I E + + W P+H GI GN + D
Sbjct: 514 SKIVNQIIEEMIKKEAIY-VAWVPAHKGIGGNQEVD 548
>1pzx_A Hypothetical protein APC36103; structural genomics, two domains
containing mixed alpha/beta structures, PSI; HET: PLM;
2.00A {Geobacillus stearothermophilus} SCOP: c.119.1.1
Length = 289
Score = 27.9 bits (63), Expect = 4.5
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 93 EVRGGKYEVGDKVRGRRR 110
V G +K RGR++
Sbjct: 195 HVEDGALIPLEKWRGRKK 212
>3nyi_A FAT acid-binding protein; stearic acid, DEGV family protein,
structural genomics, PSI- protein structure initiative;
HET: STE; 1.90A {Eubacterium ventriosum}
Length = 297
Score = 28.0 bits (63), Expect = 5.4
Identities = 4/18 (22%), Positives = 8/18 (44%)
Query: 93 EVRGGKYEVGDKVRGRRR 110
++ G +G R R +
Sbjct: 198 IMKDGDIGLGGIGRNRNK 215
>2dt8_A DEGV family protein; fatty acid binding, structural genomics,
NPPSFA, natio project on protein structural and
functional analyses; HET: PLM; 1.48A {Thermus
thermophilus}
Length = 280
Score = 27.9 bits (63), Expect = 5.5
Identities = 4/20 (20%), Positives = 10/20 (50%)
Query: 93 EVRGGKYEVGDKVRGRRRTV 112
++ G+ E + RG ++
Sbjct: 189 TLKEGRVEAAGRARGEKKAR 208
>3fys_A Protein DEGV; fatty acid-binding, EDD fold, fatty acid-binding
protein; HET: PLM; 2.50A {Bacillus subtilis}
Length = 315
Score = 27.6 bits (62), Expect = 6.8
Identities = 3/18 (16%), Positives = 7/18 (38%)
Query: 93 EVRGGKYEVGDKVRGRRR 110
+K+R R++
Sbjct: 225 HFDNKVIVPFEKIRTRKK 242
>2deb_A CPT II, carnitine O-palmitoyltransferase II, mitochondrial; central
six-stranded beta-sheet; HET: BOG COA PLM; 1.60A {Rattus
norvegicus} PDB: 2fw3_A* 2fyo_A 2rcu_A* 2h4t_A*
Length = 653
Score = 27.9 bits (61), Expect = 7.1
Identities = 17/112 (15%), Positives = 32/112 (28%), Gaps = 7/112 (6%)
Query: 233 INPSENKLRRIKSTTTPWKTSSQKARLDEVCLMRMRIGHTKITHSHLFK-----REERPI 287
+ P L KS T +K + + + S F+ R RP
Sbjct: 166 LEPEVFHLNPSKSDTDAFKRLIRFVPPSLSWYGAYLVNAYPLDMSQYFRLFNSTRIPRPN 225
Query: 288 CDSCHEPLTVEHIILHCNKLRFRPPSFLEESTQDILSDQYGQLDTVNNLNDS 339
D H+++ + ++ + L + L+DS
Sbjct: 226 RDELFTDTKARHLLVLRKGHFYVFDVLDQDGNIVNPLEIQAHLKYI--LSDS 275
>2g7z_A Conserved hypothetical protein SPY1493; long-fatty acid binding
protein, lipid binding protein, PSI, structural
genomics; HET: MSE HXA; 2.05A {Streptococcus pyogenes}
Length = 282
Score = 27.5 bits (62), Expect = 7.3
Identities = 3/18 (16%), Positives = 8/18 (44%)
Query: 93 EVRGGKYEVGDKVRGRRR 110
++ + + K RG +
Sbjct: 194 ALKNDELKTLVKGRGNKT 211
>1mgp_A Hypothetical protein TM841; two domain structure with mixed
alpha/beta structures in BOTH domains, structural
genomics; HET: PLM; 2.00A {Thermotoga maritima} SCOP:
c.119.1.1 PDB: 1vpv_A*
Length = 313
Score = 27.2 bits (61), Expect = 7.8
Identities = 5/20 (25%), Positives = 10/20 (50%)
Query: 93 EVRGGKYEVGDKVRGRRRTV 112
+ G+ KVRG ++ +
Sbjct: 219 HIENGELIPYRKVRGDKKAI 238
>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ at polymerase, DNA-binding protein;
HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP:
a.80.1.1 c.37.1.20
Length = 516
Score = 27.5 bits (61), Expect = 8.3
Identities = 7/37 (18%), Positives = 14/37 (37%), Gaps = 2/37 (5%)
Query: 279 LFKREERPICDSCHEPLT--VEHIILHCNKLRFRPPS 313
++ P+ C+E + C ++FR P
Sbjct: 174 FCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPD 210
>2cjp_A Epoxide hydrolase; HET: PG4 VPR; 1.95A {Solanum tuberosum} PDB:
3cxu_A*
Length = 328
Score = 27.4 bits (61), Expect = 9.0
Identities = 12/32 (37%), Positives = 13/32 (40%), Gaps = 4/32 (12%)
Query: 17 PSLRGVGKSQQPSEYQPRETLLNFGIWDLVGD 48
P LRG G + P F I LVGD
Sbjct: 64 PDLRGYGDTTGA----PLNDPSKFSILHLVGD 91
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
0.314 0.134 0.403
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: 5,587,812
Number of extensions: 328683
Number of successful extensions: 646
Number of sequences better than 10.0: 1
Number of HSP's gapped: 646
Number of HSP's successfully gapped: 25
Length of query: 368
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 273
Effective length of database: 4,049,298
Effective search space: 1105458354
Effective search space used: 1105458354
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: 42 (22.0 bits)
S2: 58 (26.0 bits)