RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy874
(191 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 = 78.8 bits (195), Expect = 4e-19
Identities = 34/70 (48%), Positives = 45/70 (64%), Gaps = 1/70 (1%)
Query: 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
+ VVV+TDG C NG+ AG GVY+G +PLNV ++ GR TN AEI A A++QA
Sbjct: 6 DFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQA 65
Query: 65 KSAN-EKVKL 73
K+ N K+ L
Sbjct: 66 KTQNINKLVL 75
>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 = 54.1 bits (130), Expect = 9e-10
Identities = 16/69 (23%), Positives = 23/69 (33%), Gaps = 3/69 (4%)
Query: 3 PDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALK 62
PD +TDG+ AG V + A + + AE+ ALK
Sbjct: 20 PDADYTWYTDGSSFLQEGQR-RAGAAVTTE--TEVIWARALPAGTSAQRAELIALTQALK 76
Query: 63 QAKSANEKV 71
A+ V
Sbjct: 77 MAEGKKLNV 85
>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 = 51.2 bits (123), Expect = 8e-09
Identities = 19/82 (23%), Positives = 30/82 (36%), Gaps = 7/82 (8%)
Query: 1 MDPDNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKV----TGRVTNNNAEIQG 56
MD V+TDG+ NG+ Y A + N EI
Sbjct: 1 MDDRTEYDVYTDGSY-VNGQYAW--AYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAA 57
Query: 57 AIHALKQAKSANEKVKLKRSYN 78
A++A+K+A K+++ Y
Sbjct: 58 ALYAVKKASQLGVKIRILHDYA 79
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of
RNA/DNA hybrid; 1.40A {Uncultured organism}
Length = 140
Score = 49.8 bits (120), Expect = 2e-08
Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 16/97 (16%)
Query: 5 NHVVVFTDGACPRN-GKVGASAGYGV--YFGENNPLNVAGKVTGRVTNNNAEIQGAIHAL 61
N ++++TDG N G AG GV + N L+ + G TNN AE + I AL
Sbjct: 2 NKIIIYTDGGARGNPGP----AGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRAL 57
Query: 62 KQAKSANEKVKLKRS--YNDT---HAQK----KVRNV 89
+ + +K+ D+ Q KV+
Sbjct: 58 EDLQMFGDKLVDMEVEVRMDSELIVRQMQGVYKVKEP 94
>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 = 48.7 bits (117), Expect = 6e-08
Identities = 15/62 (24%), Positives = 20/62 (32%), Gaps = 6/62 (9%)
Query: 5 NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
+ DGA R K+G G V T TN E+Q AL+ +
Sbjct: 11 GAETFYVDGAANRETKLG---KAGYVTNRGRQKVVTLTDT---TNQKTELQAIYLALQDS 64
Query: 65 KS 66
Sbjct: 65 GL 66
>1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE
motif, hydrolase; 1.50A {Bacillus halodurans} SCOP:
c.55.3.1 PDB: 1zbi_A 2g8u_A 2g8i_A 2g8h_A 2g8k_A 2g8f_A
2g8v_A 2g8w_A 3ey1_A* 1zbl_A 3d0p_A* 3i8d_A* 2r7y_A*
Length = 142
Score = 44.8 bits (106), Expect = 2e-06
Identities = 13/80 (16%), Positives = 22/80 (27%), Gaps = 4/80 (5%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
+ D N + Y + + + TNN E +H L+ K
Sbjct: 12 ESLSVDVGSQGNPGIV---EYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKE 68
Query: 67 ANEKVKLKR-SYNDTHAQKK 85
N + + S K
Sbjct: 69 RNSRKPIYSNSQTAIKWVKD 88
>2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, D stranded
RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus
tokodaii} PDB: 3aly_A
Length = 149
Score = 43.1 bits (102), Expect = 6e-06
Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 6/64 (9%)
Query: 7 VVVFTDGACPRNGKVGASAGYG--VYFGENNPLNVA---GKVTGRVTNNNAEIQGAIHAL 61
++ + DG C G A +G +Y + TNN AE G I +
Sbjct: 2 IIGYFDGLC-EPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLM 60
Query: 62 KQAK 65
+
Sbjct: 61 ETML 64
>3hst_B Protein RV2228C/MT2287; ribonuclease H1, RV2228C N-terminal
domain, fusion protein, maltose binding protein, HYDR;
HET: MLR TAR; 2.25A {Mycobacterium tuberculosis}
Length = 141
Score = 41.9 bits (99), Expect = 2e-05
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENN-PLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
VV+ DG N A G V+ +++ L + + GR TNN AE +G I L A
Sbjct: 3 KVVIEADGGSRGNPG-PAGYGAVVWTADHSTVLAESKQAIGRATNNVAEYRGLIAGLDDA 61
Query: 65 K 65
Sbjct: 62 V 62
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 39.5 bits (93), Expect = 1e-04
Identities = 23/72 (31%), Positives = 29/72 (40%), Gaps = 9/72 (12%)
Query: 1 MDPDNHVVVFTDGACPRNGKVGASAGYGV---YFGENNPLNVAGKVTGRVTNNNAEIQGA 57
P V +FTDGAC N G G+ + L+ T TNN E++ A
Sbjct: 3 PSPRKRVALFTDGACLGNPGPG---GWAALLRFHAHEKLLSGGEACT---TNNRMELKAA 56
Query: 58 IHALKQAKSANE 69
I LK K E
Sbjct: 57 IEGLKALKEPCE 68
>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}
Length = 540
Score = 38.8 bits (90), Expect = 6e-04
Identities = 6/31 (19%), Positives = 15/31 (48%)
Query: 107 VISVGIPFPSIQDENVKLKRSYNDTHAQKKG 137
++ G+P+P++ D+ V+ + K
Sbjct: 456 LVLAGLPYPNVSDDMVRKRIERLSKLTGKDE 486
Score = 32.6 bits (74), Expect = 0.067
Identities = 6/26 (23%), Positives = 13/26 (50%)
Query: 137 GIPFPSIQDEKVKLKRSYNDTHAQKK 162
G+P+P++ D+ V+ + K
Sbjct: 460 GLPYPNVSDDMVRKRIERLSKLTGKD 485
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 37.5 bits (88), Expect = 6e-04
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 15/68 (22%)
Query: 1 MDPDNHVVVFTDGAC---PRNGKVGASAGYGV---YFGENNPLNVAGKVTGRVTNNNAEI 54
M + +FTDG+C P G GYG+ Y G ++ +T TNN E+
Sbjct: 1 MTELKLIHIFTDGSCLGNPGPG------GYGIVMNYKGHTKEMSDGFSLT---TNNRMEL 51
Query: 55 QGAIHALK 62
I AL+
Sbjct: 52 LAPIVALE 59
>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer
aging, hydrolase; HET: FLC; 2.00A {Sulfolobus
acidocaldarius} PDB: 3crw_1*
Length = 551
Score = 37.7 bits (87), Expect = 0.001
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 107 VISVGIPFPSIQDENVKLKRSYNDTHAQKKG 137
V+ VGIP+P D L + + ++
Sbjct: 466 VVIVGIPYPPPDDYLKILAQRVSLKMNRENE 496
Score = 31.5 bits (71), Expect = 0.15
Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 137 GIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSV-AMR 172
GIP+P D L + + ++ + + A+
Sbjct: 470 GIPYPPPDDYLKILAQRVSLKMNRENEEFLFKIPALV 506
>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 = 35.9 bits (84), Expect = 0.002
Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 10/72 (13%)
Query: 5 NHVVVFTDGACPRNGKVGASAGYGV---YFGENNPLNVAGKVTGRVTNNNAEIQGAIHAL 61
V +FT G+ N G GYG Y G + T TNN E+ AI AL
Sbjct: 3 KQVEIFTAGSALGNPGPG---GYGAILRYRGREKTFSAGYTRT---TNNRMELMAAIVAL 56
Query: 62 KQAKSANEKVKL 73
+ K + +V L
Sbjct: 57 EALKE-HAEVIL 67
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 35.5 bits (83), Expect = 0.003
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 15/65 (23%)
Query: 4 DNHVVVFTDGAC---PRNGKVGASAGYGV---YFGENNPLNVAGKVTGRVTNNNAEIQGA 57
+ + ++TDGA P G G+G Y ++ T TNN E+ A
Sbjct: 2 EKTITIYTDGAASGNPGKG------GWGALLMYGSSRKEISGYDPAT---TNNRMELMAA 52
Query: 58 IHALK 62
I L+
Sbjct: 53 IKGLE 57
>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase,
nucleotide excision repair,; 2.20A {Thermoplasma
acidophilum} PDB: 2vsf_A*
Length = 620
Score = 30.4 bits (69), Expect = 0.30
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 4/34 (11%)
Query: 107 VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPF 140
+I G+PFP N L Y K G +
Sbjct: 520 IILAGLPFPRPDAINRSLFDYYER----KYGKGW 549
>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 = 30.1 bits (68), Expect = 0.41
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 6/57 (10%)
Query: 10 FTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
+ DGA R K+G AGY G + + TN E+Q AL+ +
Sbjct: 443 YVDGAANRETKLG-KAGYVTNKGRQKVVPLTN-----TTNQKTELQAIYLALQDSGL 493
>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 = 30.1 bits (68), Expect = 0.41
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 10 FTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
+TDG+C R K G AGY G++ + TN AE++ AL +
Sbjct: 440 YTDGSCNRQSKEG-KAGYVTDRGKDKVKKLEQ-----TTNQQAELEAFAMALTDSGP 490
>2h30_A Thioredoxin, peptide methionine sulfoxide reductase MSRA/MSRB;
reduced, thiol-disulfide exchange, oxidoreductase; 1.60A
{Neisseria gonorrhoeae} PDB: 2jzr_A 2jzs_A 2k9f_A 2fy6_A
Length = 164
Score = 28.6 bits (64), Expect = 0.89
Identities = 7/50 (14%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 106 DVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQDEKVKLKRSYN 155
++I+V P + ++ + ++ Y + P + D + ++ N
Sbjct: 73 NLITVASPGFLHEKKDGEFQKWYAGLN----YPKLPVVTDNGGTIAQNLN 118
>2atm_A Hyaluronoglucosaminidase; beta-alpha-barrels, hydrolase; HET: MES;
2.00A {Vespula vulgaris}
Length = 331
Score = 27.9 bits (62), Expect = 2.3
Identities = 8/48 (16%), Positives = 18/48 (37%), Gaps = 5/48 (10%)
Query: 140 FPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYKLLVSGYF 187
PS+ +++ V+ A+RI+ + + V Y+
Sbjct: 219 LPSVY-----VRQELTPDQRIGLVQGRVKEAVRISNNLKHSPKVLSYW 261
>3js4_A Superoxide dismutase; niaid, ssgcid, seattle structural genomics
center for infect disease, GRAM-negative bacteria;
1.95A {Anaplasma phagocytophilum}
Length = 227
Score = 26.1 bits (58), Expect = 6.6
Identities = 8/42 (19%), Positives = 16/42 (38%), Gaps = 2/42 (4%)
Query: 47 VTNNNAEIQGAIHALKQAKSANEKVKLKRSYNDTHAQKKVRN 88
V N + G +S + V +++N A + + N
Sbjct: 54 VDVLNKLVVGTEFEGLGNESLGDIV--VKAHNSGSAGRAIFN 93
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 0.130 0.366
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,835,812
Number of extensions: 160428
Number of successful extensions: 259
Number of sequences better than 10.0: 1
Number of HSP's gapped: 247
Number of HSP's successfully gapped: 26
Length of query: 191
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 103
Effective length of database: 4,244,745
Effective search space: 437208735
Effective search space used: 437208735
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (24.7 bits)