RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2786
(198 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 = 35.4 bits (82), Expect = 0.003
Identities = 8/41 (19%), Positives = 15/41 (36%)
Query: 32 NKPKPLCLRVHLLCYGKQLAFLWCPSHTGIQGNEAVDRAAR 72
+ Y +F +H+G + N+ VD A+
Sbjct: 92 KNEFTQAYAKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAK 132
>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 = 35.0 bits (80), Expect = 0.014
Identities = 48/272 (17%), Positives = 82/272 (30%), Gaps = 111/272 (40%)
Query: 2 SY--AVKIASCP-ANPTYSLLF---PDNIDADIYPPNKPKPLCLRVHLLCYGKQ------ 49
+Y A +A P + S LF + +A + +G Q
Sbjct: 125 NYITARIMAKRPFDKKSNSALFRAVGEG-NAQLV--------------AIFGGQGNTDDY 169
Query: 50 ---LAFLWCPSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFIHKLIKDL--WQNS 104
L L+ H + + + +A +L L + + K F L ++ W +
Sbjct: 170 FEELRDLYQTYHVLVG--DLIKFSA----ETLSELIRTTLDAEKVFTQGL--NILEWLEN 221
Query: 105 WSNIPNCNKLKSIK---PVIGPWPSSDRQNRHEEVVICR--------MRIGHTRATHGH- 152
SN P+ + L SI P+IG Q H VV + +R + + GH
Sbjct: 222 PSNTPDKDYLLSIPISCPLIGVI-----QLAHY-VVTAKLLGFTPGELR-SYLKGATGHS 274
Query: 153 ----------------------------LFK---RA---------PPS----TCRCGET- 167
LF R PPS + E
Sbjct: 275 QGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGV 334
Query: 168 ----LSVQHILTCTLHGHIR---ASLPAPPAL 192
LS+ ++ + ++ + LPA +
Sbjct: 335 PSPMLSISNLTQEQVQDYVNKTNSHLPAGKQV 366
Score = 28.5 bits (63), Expect = 2.1
Identities = 7/17 (41%), Positives = 8/17 (47%), Gaps = 1/17 (5%)
Query: 177 TL-HGHIRASLPAPPAL 192
TL HG + L P A
Sbjct: 10 TLSHGSLEHVLLVPTAS 26
>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 = 32.9 bits (75), Expect = 0.036
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 42 HLLCYGKQLAFLWCPSHTG-----IQGNEAVDRAAR 72
L K+L+ + CP H +GN D+AAR
Sbjct: 116 KALFLPKRLSIIHCPGHQKGNSAEARGNRMADQAAR 151
>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 = 0.057
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 44 LCYGKQLAFLWCPSHTGIQGNEAVDRAARN 73
L G + ++ P H+G GNE DR AR
Sbjct: 118 LTQGMDIQWMHVPGHSGFIGNEEADRLARE 147
>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 = 0.11
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 54 WCPSHTGIQGNEAVDR 69
W P+H GI GNE VD+
Sbjct: 537 WVPAHKGIGGNEQVDK 552
>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 = 10/20 (50%), Positives = 12/20 (60%)
Query: 54 WCPSHTGIQGNEAVDRAARN 73
W P+H GI GNE VD+
Sbjct: 124 WVPAHKGIGGNEQVDKLVSA 143
>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 = 30.5 bits (69), Expect = 0.39
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 47 GKQLAFL-WCPSHTGIQGNEAVDR 69
K+ ++ W P+H GI GN+ VD
Sbjct: 526 KKEAIYVAWVPAHKGIGGNQEVDH 549
>3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 259
Score = 26.8 bits (60), Expect = 4.9
Identities = 5/15 (33%), Positives = 6/15 (40%)
Query: 147 RATHGHLFKRAPPST 161
+ THG R S
Sbjct: 175 QMTHGSKSHRQLGSI 189
>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 = 25.5 bits (57), Expect = 9.1
Identities = 9/30 (30%), Positives = 11/30 (36%)
Query: 44 LCYGKQLAFLWCPSHTGIQGNEAVDRAARN 73
Q+ + W H G NE D AR
Sbjct: 110 ALGQHQIKWEWVKGHAGHPENERADELARA 139
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 25.6 bits (57), Expect = 9.6
Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 44 LCYGKQLAFLWCPSHTGIQGNEAVDRAARN--PSASLPPLKLCSPEDFKP 91
++ F + HTG NE VDR AR S + P +P F
Sbjct: 115 AMAPHRVRFHFVKGHTGHPENERVDREARRQAQSQAKTPCPPRAPTLFHE 164
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
0.321 0.137 0.456
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,141,271
Number of extensions: 173113
Number of successful extensions: 303
Number of sequences better than 10.0: 1
Number of HSP's gapped: 303
Number of HSP's successfully gapped: 15
Length of query: 198
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 109
Effective length of database: 4,216,824
Effective search space: 459633816
Effective search space used: 459633816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.0 bits)