RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16807
(220 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 = 35.8 bits (83), Expect = 0.003
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 28 LSDSYWTVVSFLWIPSHVGIRENNLVDEAAR 58
L + Y + SF + +H G N+ VD A+
Sbjct: 102 LMNQYRGIYSFEKVKAHSGNEFNDYVDMKAK 132
>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 = 35.2 bits (80), Expect = 0.013
Identities = 42/239 (17%), Positives = 81/239 (33%), Gaps = 70/239 (29%)
Query: 42 PSHVGIRENNLVDEAAR-----NSNEAPLSTIC-------TADDYRAVFKKLQLEVWAFA 89
P + I ++ D A + N L+TI +YR +F +L + F
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV----FP 382
Query: 90 DDYRAVFKKVQLEV-WAK-PWRENQLTGQKLKKIKCDTRKWKSSTR---DVRAEEIVVCR 144
+ + L + W + + KL K ++ K ST + E +
Sbjct: 383 PSAH-IPTIL-LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLEL----K 436
Query: 145 LRIGHCLATHQYLLERQNPPACHLCNEVPIT---------IKHWLLECP---RLNALRRK 192
+++ + A H+ +++ N P +++ I H L R+ R
Sbjct: 437 VKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMV 496
Query: 193 ---FKF---------------GSCLKT----------ILKDD---EIIIDSCVNFLKEA 220
F+F GS L T I +D E ++++ ++FL +
Sbjct: 497 FLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKI 555
>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 = 32.9 bits (76), Expect = 0.035
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 36 VSFLWIPSHVGIRENNLVDEAARN 59
V W+P+H GI N VD+
Sbjct: 120 VYLAWVPAHKGIGGNEQVDKLVSA 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 = 32.2 bits (74), Expect = 0.065
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 36 VSFLWIPSHVGIRENNLVDEAARN 59
+ ++ +P H G N D AR
Sbjct: 124 IQWMHVPGHSGFIGNEEADRLARE 147
>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 = 30.9 bits (71), Expect = 0.17
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 36 VSFLWIPSHVGIRENNLVDEAARNSNEAP 64
+ + W+ H G EN DE AR + P
Sbjct: 116 IKWEWVKGHAGHPENERADELARAAAMNP 144
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 30.6 bits (70), Expect = 0.19
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 36 VSFLWIPSHVGIRENNLVDEAARNSNEAPLSTICT 70
V F ++ H G EN VD AR ++ T C
Sbjct: 121 VRFHFVKGHTGHPENERVDREARRQAQSQAKTPCP 155
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 30.1 bits (69), Expect = 0.26
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 36 VSFLWIPSHVGIRENNLVDEAAR 58
V+F + H N+ DE AR
Sbjct: 117 VTFHKVKGHSDNPYNSRADELAR 139
>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 = 30.2 bits (68), Expect = 0.29
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 5/41 (12%)
Query: 36 VSFLWIPSHVG-----IRENNLVDEAARNSNEAPLSTICTA 71
+S + P H R N + D+AAR + + T
Sbjct: 124 LSIIHCPGHQKGNSAEARGNRMADQAAREAAMKAVLETSTL 164
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 30.2 bits (69), Expect = 0.30
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 36 VSFLWIPSHVGIRENNLVDEAARN 59
+ + W+ H G EN D+ AR
Sbjct: 118 IDWRWVKGHAGHAENERCDQLARA 141
>3idu_A Uncharacterized protein; all beta-protein, structural genomics,
PSI-2, protein structure initiative; 1.70A {Pyrococcus
furiosus} PDB: 2kl6_A
Length = 127
Score = 29.6 bits (66), Expect = 0.44
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 7/48 (14%)
Query: 34 TVVSFLWIPSHVGIR-------ENNLVDEAARNSNEAPLSTICTADDY 74
V++F W P+ G+ E N V E N+N A + +
Sbjct: 76 KVLTFNWTPTQEGMYRINATVDEENTVVELNENNNVATFDVSVVLEHH 123
>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 = 29.2 bits (65), Expect = 1.3
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 17/60 (28%)
Query: 72 DDYR--AVFKKLQLEVWAFADDY-RAVFKKVQLEVWAKPWREN--QLT----GQKLKKIK 122
D Y+ + +VW AD++ + + L++ N LT G+K K+I+
Sbjct: 1634 DLYKTSKAAQ----DVWNRADNHFKDTYGFSILDI----VINNPVNLTIHFGGEKGKRIR 1685
Score = 28.1 bits (62), Expect = 3.0
Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 13/58 (22%)
Query: 173 PITIKHWLLEC----PR---LNALRRKFKFGSCL----KTILKDDEII--IDSCVNFL 217
P+T+ H LE P A + + +F L + DDE + FL
Sbjct: 8 PLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFL 65
>4a2a_A Cell division protein FTSA, putative; cell cycle, actin, divisome;
HET: ATP; 1.80A {Thermotoga maritima} PDB: 1e4g_T*
1e4f_T* 4a2b_A*
Length = 419
Score = 27.7 bits (62), Expect = 3.0
Identities = 7/32 (21%), Positives = 13/32 (40%)
Query: 181 LECPRLNALRRKFKFGSCLKTILKDDEIIIDS 212
L+ + R G+ + LK++EI
Sbjct: 249 LDTSFEESERLIITHGNAVYNDLKEEEIQYRG 280
>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 = 27.2 bits (59), Expect = 3.3
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 5/27 (18%)
Query: 79 KKLQLEVWAFADDYR---AVFKKVQLE 102
KKLQ + +ADD A+ K +E
Sbjct: 23 KKLQASLKLYADDSAPALAI--KATME 47
>1kbi_A Cytochrome B2, L-LCR; flavocytochrome B2, electron transfer,
oxidoreductase; HET: HEM FMN; 2.30A {Saccharomyces
cerevisiae} SCOP: c.1.4.1 d.120.1.1 PDB: 1fcb_A* 1lco_A*
1ldc_A* 1sze_A* 2oz0_A* 1szf_A* 1szg_A* 1ltd_A* 1kbj_A*
1qcw_A* 3ks0_A*
Length = 511
Score = 27.3 bits (61), Expect = 4.8
Identities = 12/71 (16%), Positives = 25/71 (35%), Gaps = 11/71 (15%)
Query: 42 PSHVGIRENNLVDEAARNSNEAPLSTICTADDYRAVFKK-LQLEVWAF----ADDY---- 92
P G + ++ + S PL I D+ + + L + WA+ A+D
Sbjct: 96 PYAPGETKEDIARKEQLKSLLPPLDNIINLYDFEYLASQTLTKQAWAYYSSGANDEVTHR 155
Query: 93 --RAVFKKVQL 101
+ ++
Sbjct: 156 ENHNAYHRIFF 166
>1iak_A MHC class II I-AK; histocompatibility antigen, peptide complex,
histocompa antigen I-AK; HET: NAG; 1.90A {Mus musculus}
SCOP: b.1.1.2 d.19.1.1 PDB: 1d9k_C* 1k2d_A* 1jl4_A
2pxy_C 1u3h_C 2z31_C 1muj_A* 1lnu_A* 3c5z_C 3c60_C
3c6l_C 3rdt_C 2iad_A 1iao_A 1es0_A 3cup_A* 3mbe_A*
1f3j_A*
Length = 199
Score = 25.9 bits (57), Expect = 9.7
Identities = 9/89 (10%), Positives = 21/89 (23%), Gaps = 16/89 (17%)
Query: 90 DDYRAVFKKVQLEVWAKPWRENQLTGQKLKKIKCDTRKWKSSTRDVRAEEIVVCRLRIGH 149
D+ V + VW P R+++ + I + +
Sbjct: 33 DELFYVDLDKKETVWMLPEFAQL-------------RRFEP---QGGLQNIATGKHNLEI 76
Query: 150 CLATHQYLLERQNPPACHLCNEVPITIKH 178
P + + P+ +
Sbjct: 77 LTKRSNSTPATNEAPQATVFPKSPVLLGQ 105
>3oh8_A Nucleoside-diphosphate sugar epimerase (SULA FAMI; DUF1731_C,
northeast structural genomics consortium, NESG, C
PSI-biology; 2.00A {Corynebacterium glutamicum}
Length = 516
Score = 26.2 bits (58), Expect = 9.9
Identities = 8/39 (20%), Positives = 13/39 (33%)
Query: 126 RKWKSSTRDVRAEEIVVCRLRIGHCLATHQYLLERQNPP 164
R W+ +T V +R G L+ +L
Sbjct: 283 RDWEHATAPASDAGKRVAFIRTGVALSGRGGMLPLLKTL 321
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 0.136 0.444
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,479,982
Number of extensions: 194354
Number of successful extensions: 422
Number of sequences better than 10.0: 1
Number of HSP's gapped: 419
Number of HSP's successfully gapped: 21
Length of query: 220
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 130
Effective length of database: 4,188,903
Effective search space: 544557390
Effective search space used: 544557390
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: 55 (25.0 bits)