RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16114
(202 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 = 41.2 bits (97), Expect = 4e-05
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 21 TNPLVSKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARNPTDLDQLK 73
++AY L+ F +H G N+ VD A++ + L+
Sbjct: 91 AKNEFTQAY--AKLMNQYRGIYSFEKVKAHSGNEFNDYVDMKAKSALGIRDLE 141
>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 = 36.4 bits (83), Expect = 0.005
Identities = 26/135 (19%), Positives = 41/135 (30%), Gaps = 39/135 (28%)
Query: 11 ALSALSNIKFTNPLVSKAY--SCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARNPTD 68
L L N++ N A+ SC LLT+ K V + + +D + T
Sbjct: 246 CLLVLLNVQ--NAKAWNAFNLSCKILLTTRFKQVTDFLSAAT---TTHISLDHHSMTLTP 300
Query: 69 LDQLKL------CSPDDFK-------PLAASLV---RKEWQDQWNLVPVTNKLKSIKPLI 112
+ L C P D P S++ ++ W+
Sbjct: 301 DEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD--------------- 345
Query: 113 TNWDTSNQENRTKEI 127
NW N + T I
Sbjct: 346 -NWKHVNCDKLTTII 359
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 34.5 bits (80), Expect = 0.008
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 37 SNNKDVRFMWCPSHCGIRGNEDVDQAARN 65
+ D+++M P H G GNE+ D+ AR
Sbjct: 119 TQGMDIQWMHVPGHSGFIGNEEADRLARE 147
>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 = 33.3 bits (77), Expect = 0.018
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 41 DVRFMWCPSHCGIRGNEDVDQAARN 65
V W P+H GI GNE VD+
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSA 143
>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 = 33.7 bits (77), Expect = 0.021
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 5/33 (15%)
Query: 37 SNNKDVRFMWCPSHCG-----IRGNEDVDQAAR 64
K + + CP H RGN DQAAR
Sbjct: 119 FLPKRLSIIHCPGHQKGNSAEARGNRMADQAAR 151
>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 = 32.8 bits (75), Expect = 0.070
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 46 WCPSHCGIRGNEDVDQ 61
W P+H GI GNE VD+
Sbjct: 537 WVPAHKGIGGNEQVDK 552
>3nrt_A Putative ryanodine receptor; PSI-2, protein structure initiative,
structural genomics, MI center for structural genomics
(MCSG); 2.54A {Bacteroides thetaiotaomicron}
Length = 103
Score = 29.6 bits (66), Expect = 0.27
Identities = 13/98 (13%), Positives = 28/98 (28%), Gaps = 9/98 (9%)
Query: 60 DQAARNPTDLDQLKLCSPDDFKPLAASLVRKE---W-----QDQWNLVPVTNKLKSIKPL 111
++ P +D + P+ L+ + W + W + + P
Sbjct: 7 NKLDYIPEPMDLSLVDLPESLIQLSERIAENVHEVWAKARIDEGWTYGEKRDDIHKKHPC 66
Query: 112 ITNWDTSNQENRTKEITLTRMRIGHTRLTHGFIFTKTD 149
+ +D +E + + GF K D
Sbjct: 67 LVPYDELPEEEKEYDRNTAM-NTIKMVKKLGFRIEKED 103
>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 = 0.45
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 46 WCPSHCGIRGNEDVDQ 61
W P+H GI GN++VD
Sbjct: 534 WVPAHKGIGGNQEVDH 549
>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 = 29.1 bits (64), Expect = 0.57
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 8/31 (25%)
Query: 61 QAARNPTDLD-QLKLCSPDDFKP-LA--ASL 87
QA + L LKL + D P LA A++
Sbjct: 20 QALKK---LQASLKLYADDS-APALAIKATM 46
>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 = 28.6 bits (65), Expect = 0.83
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 41 DVRFMWCPSHCGIRGNEDVDQ----AARNPTDLDQ 71
+++ W H G NE D+ AA NPT D
Sbjct: 115 QIKWEWVKGHAGHPENERADELARAAAMNPTLEDT 149
>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 = 1.0
Identities = 27/208 (12%), Positives = 67/208 (32%), Gaps = 60/208 (28%)
Query: 5 GNGFISALSALSNIKFTNPLVSKAYSCWDLLTSN-NKDVRFM-WCPSHCGIRGNEDVDQA 62
G ++A+ +++ S W+ + K + + + G+R E
Sbjct: 274 SQGLVTAV-----------AIAETDS-WESFFVSVRKAITVLFFI----GVRCYEAYPNT 317
Query: 63 ARNPTDLDQLKLCSPDDFK----PLAASLVRKEWQDQWNLVPVTNKLKSIKPLITNWDTS 118
+ P+ L+ S ++ + P+ + + Q+Q ++ + ++
Sbjct: 318 SLPPSILED----SLENNEGVPSPMLS--ISNLTQEQ------------VQDYVNKTNSH 359
Query: 119 NQENRTKEITLT---RMRI--GHTRLTHGFIF--------TKTDPPNCPCGEHLSVRHIL 165
+ EI+L + + G + +G + D P S R +
Sbjct: 360 LPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIP----FSERKLK 415
Query: 166 TCHRHAQIRASLP-HPPSLADDVEGVKS 192
+R + + P H L + +
Sbjct: 416 FSNRFLPV--ASPFHSHLLVPASDLINK 441
Score = 28.9 bits (64), Expect = 1.5
Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 4/44 (9%)
Query: 159 LSVRHI-LTCHRHAQIRASLPHPPSLADDVEGVKSLFTYVTATP 201
S R + L+ H + L P + ++ F + P
Sbjct: 4 YSTRPLTLS---HGSLEHVLLVPTASFFIASQLQEQFNKILPEP 44
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 27.8 bits (63), Expect = 1.3
Identities = 7/24 (29%), Positives = 8/24 (33%)
Query: 41 DVRFMWCPSHCGIRGNEDVDQAAR 64
V F H N D+ AR
Sbjct: 116 RVTFHKVKGHSDNPYNSRADELAR 139
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 27.6 bits (62), Expect = 2.1
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 41 DVRFMWCPSHCGIRGNEDVDQAAR 64
VRF + H G NE VD+ AR
Sbjct: 120 RVRFHFVKGHTGHPENERVDREAR 143
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 28.3 bits (63), Expect = 2.1
Identities = 22/112 (19%), Positives = 43/112 (38%), Gaps = 28/112 (25%)
Query: 18 IKFTN-PLVSKAYSCW-DLLTS---NNKDV--RF----MWCPSHCGIRGNE----DVDQA 62
I + N L + Y+ W D T ++KDV ++ + H GIR E +
Sbjct: 861 ISYHNGNLKGRPYTGWVDSKTKEPVDDKDVKAKYETSIL---EHSGIRLIEPELFNGY-- 915
Query: 63 ARNPTDLDQLKLCSPD-DFKPLAAS-----LVRKEWQDQWNLVPVTNKLKSI 108
NP + ++ + D +P AS + + D+ ++ + +
Sbjct: 916 --NPEKKEMIQEVIVEEDLEPFEASKETAEQFKHQHGDKVDIFEIPETGEYS 965
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 27.1 bits (61), Expect = 2.5
Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 1/33 (3%)
Query: 34 LLTSNNK-DVRFMWCPSHCGIRGNEDVDQAARN 65
L + + + W H G NE DQ AR
Sbjct: 109 LDKAAQLHQIDWRWVKGHAGHAENERCDQLARA 141
>1kbl_A PPDK, pyruvate phosphate dikinase; transferase, phosphotransferase;
1.94A {Clostridium symbiosum} SCOP: c.1.12.2 c.8.1.1
d.142.1.5 PDB: 1kc7_A* 1dik_A 1ggo_A 1jde_A 2dik_A
2r82_A 2fm4_A
Length = 873
Score = 26.6 bits (59), Expect = 7.8
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 57 EDVDQAARNPTDLDQLKLCSPDDFKPL 83
EDV R P + QL+ PD +K
Sbjct: 278 EDVVAGVRTPQPITQLENDMPDCYKQF 304
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
0.319 0.134 0.433
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: 3,046,019
Number of extensions: 164986
Number of successful extensions: 323
Number of sequences better than 10.0: 1
Number of HSP's gapped: 322
Number of HSP's successfully gapped: 18
Length of query: 202
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 113
Effective length of database: 4,216,824
Effective search space: 476501112
Effective search space used: 476501112
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 (21.8 bits)
S2: 55 (24.8 bits)