RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7660
(250 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 = 42.3 bits (100), Expect = 2e-05
Identities = 13/93 (13%), Positives = 23/93 (24%), Gaps = 13/93 (13%)
Query: 24 NNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSI-----ANKNTTIPLIAHI 78
E+ A ++ + V I+ D A T +
Sbjct: 45 AATMRNVAGEIAAALYAVKKASQLG-VKIRILHDYAGIAFWATGEWKAKNEFTQAYAKLM 103
Query: 79 LNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDR 111
+F +H+G N+ VD
Sbjct: 104 -------NQYRGIYSFEKVKAHSGNEFNDYVDM 129
>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 = 43.5 bits (102), Expect = 4e-05
Identities = 29/156 (18%), Positives = 56/156 (35%), Gaps = 39/156 (25%)
Query: 29 IFTAELLAIVFCLDSVKNRPDVNTLIVCDSM---------SALTSIANK---NTTIPLIA 76
+ E A L K++ LI D+ +AL S+A+ + + ++
Sbjct: 1736 LTLMEK-AAFEDL---KSK----GLIPADATFAGHSLGEYAALASLADVMSIESLVEVVF 1787
Query: 77 H---ILNTWYSLKSCGK-NVAFLWC-PSHTGISGNE-----IVDRATRQLDG-AEIVNLS 125
+ + G+ N + P S ++ +V+R ++ EIVN +
Sbjct: 1788 YRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNYN 1847
Query: 126 SPADLIPV--GKKYLLEKWQKSWTELIN-NKLKRIK 158
V G L+ T ++N KL++I
Sbjct: 1848 VENQQY-VAAGDLRALDT----VTNVLNFIKLQKID 1878
>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 = 43.2 bits (102), Expect = 4e-05
Identities = 30/84 (35%), Positives = 39/84 (46%), Gaps = 14/84 (16%)
Query: 32 AELLAIVFCL-DSVKNRPDVNTLIVCDSMSALTSIANK--NTTIPLIAHILNTWYSLKSC 88
EL AI L DS +VN IV DS AL I + + L+ I+ +
Sbjct: 479 TELQAIYLALQDS---GLEVN--IVTDSQYALGIIQAQPDKSESELVNQIIE-----QLI 528
Query: 89 GKNVAFL-WCPSHTGISGNEIVDR 111
K +L W P+H GI GNE VD+
Sbjct: 529 KKEKVYLAWVPAHKGIGGNEQVDK 552
>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 = 40.2 bits (94), Expect = 1e-04
Identities = 20/94 (21%), Positives = 34/94 (36%), Gaps = 17/94 (18%)
Query: 32 AELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIP-----LIAHILNTWYSLK 86
AEL+A+ L + +N + DS A + + I +L
Sbjct: 66 AELIALTQALKMAE-GKKLN--VYTDSRYAFATAHVHSEGREIKNKNEILALLK----AL 118
Query: 87 SCGKNVAFLWCPSHTG-----ISGNEIVDRATRQ 115
K ++ + CP H GN + D+A R+
Sbjct: 119 FLPKRLSIIHCPGHQKGNSAEARGNRMADQAARE 152
>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 = 40.5 bits (95), Expect = 4e-04
Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 14/84 (16%)
Query: 32 AELLAIVFCL-DSVKNRPDVNTLIVCDSMSALTSIANK--NTTIPLIAHILNTWYSLKSC 88
AEL A L DS P VN I+ DS + +A++ + ++ I+ +
Sbjct: 476 AELEAFAMALTDS---GPKVN--IIVDSQYVMGIVASQPTESESKIVNQIIE-----EMI 525
Query: 89 GKNVAFL-WCPSHTGISGNEIVDR 111
K ++ W P+H GI GN+ VD
Sbjct: 526 KKEAIYVAWVPAHKGIGGNQEVDH 549
>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 = 39.5 bits (91), Expect = 8e-04
Identities = 46/292 (15%), Positives = 82/292 (28%), Gaps = 93/292 (31%)
Query: 1 GSKTL---QNTSCA-VYAGGTTKSYILNNINSIFT-AELLAIVF--CLD-SVKNRP---- 48
K L + + TT L++ + T E+ ++ LD ++ P
Sbjct: 265 SCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL-LLKYLDCRPQDLPREVL 323
Query: 49 DVNTLIVCDSMSALTSIANKNTTIPLIAHILNTW-YSLKSCGKNVAFLWCPSHTGISGNE 107
N L+ IA I L TW +
Sbjct: 324 TTNPR-------RLSIIAE------SIRDGLATWDNWKHVNCDKL-------------TT 357
Query: 108 IVDRATRQLDGAEI----VNLSS-PADL-IPVG----------------------KKYLL 139
I++ + L+ AE LS P IP K L+
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417
Query: 140 EKWQKSWTELINNKLKRIKPTIGPWNVSDCNSR----YEESISWSGNKCF---IDHYSHP 192
EK K T I + +K + N + Y ++ + +D Y +
Sbjct: 418 EKQPKESTISIPSIYLELKVKLE--NEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYS 475
Query: 193 YL-----------KVLPFNMFKQSYKYLMCPVIAS-----ACDSVLVSLSDF 228
++ ++ F M +++L + A S+L +L
Sbjct: 476 HIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL 527
>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 = 30.6 bits (70), Expect = 0.22
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 91 NVAFLWCPSHTGISGNEIVDRATRQ 115
V W P+H GI GNE VD+
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSA 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 = 29.5 bits (67), Expect = 0.67
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 91 NVAFLWCPSHTGISGNEIVDRATRQLDGAE 120
++ ++ P H+G GNE DR R+ GA+
Sbjct: 123 DIQWMHVPGHSGFIGNEEADRLARE--GAK 150
>2ns6_A Mobilization protein A; nickase, 5-strand antiparallel beta sheet,
metalloenzyme, hydrolase; 2.10A {Pseudomonas aeruginosa}
Length = 185
Score = 28.2 bits (62), Expect = 1.9
Identities = 9/54 (16%), Positives = 18/54 (33%)
Query: 103 ISGNEIVDRATRQLDGAEIVNLSSPADLIPVGKKYLLEKWQKSWTELINNKLKR 156
G E + + + K LE+ +++W + N L+R
Sbjct: 129 NDGIERPAAQWFKRYNGKTPEKGGAQKTEALKPKAWLEQTREAWADHANRALER 182
>3cwv_A DNA gyrase, B subunit, truncated; structural genomics, unknown
function, B-subunit binding, isomerase,
nucleotide-binding, topoisomerase; HET: DNA; 1.95A
{Myxococcus xanthus}
Length = 369
Score = 27.1 bits (61), Expect = 5.7
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 230 VVLALSERTRVRVW 243
V LALS R +V +W
Sbjct: 104 VSLALSSRYQVDIW 117
>3szy_A Phosphonoacetate hydrolase; alkaline phosphatase superfamily; 1.35A
{Sinorhizobium meliloti} PDB: 3szz_A 3t00_A 3t01_A
3t02_A
Length = 427
Score = 27.1 bits (59), Expect = 6.4
Identities = 31/201 (15%), Positives = 55/201 (27%), Gaps = 33/201 (16%)
Query: 18 TKSYILNNINSIFTAELLAIVFCLDSVKNRPD-VNTLIVCDSMSALTSIANKNTTIPLIA 76
+K + N + AI CLD P ++ I M AL I + +
Sbjct: 8 SKISVTVNGRRYPWPRVPAIAVCLDGC--EPAYLDAAIDAGLMPALKRIKERGAVRLAHS 65
Query: 77 HI----LNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQLDGAEIVNLSSPADLIP 132
I S+ + G P+ GI GN + + +T E V ++ P
Sbjct: 66 VIPSFTNPNNLSI-ATGS------PPAVHGICGNYLYEPSTG-----EEVMMNDP----- 108
Query: 133 VGKKYLLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRYEESISWSGNKCFIDHYSHP 192
K+ ++ T + + + G
Sbjct: 109 --------KFLRAPTIFQAFYDAGARVAVVTAKDKLRALLGKGLRFDEGRA-VCFSSEKS 159
Query: 193 YLKVLPFNMFKQSYKYLMCPV 213
+ + +L PV
Sbjct: 160 DKATRAEHGIDNASAWLGRPV 180
>2eqa_A Hypothetical protein ST1526; YRDC/RIBB fold, YRDC domain, SUA5
domain, structural genomics, NPPSFA; HET: AMP; 1.80A
{Sulfolobus tokodaii} PDB: 3aje_A* 4e1b_A*
Length = 352
Score = 26.8 bits (60), Expect = 7.2
Identities = 12/38 (31%), Positives = 15/38 (39%), Gaps = 4/38 (10%)
Query: 43 SVKNRPDVNTLIV-CDSMSALTSIANKNTTIPLIAHIL 79
KNRP N LIV + L +A IP +
Sbjct: 55 QAKNRPVDNPLIVHIADFNQLFEVA---KDIPDKVLEI 89
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
0.320 0.133 0.414
Gapped
Lambda K H
0.267 0.0492 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,700,965
Number of extensions: 202352
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 411
Number of HSP's successfully gapped: 18
Length of query: 250
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 159
Effective length of database: 4,160,982
Effective search space: 661596138
Effective search space used: 661596138
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: 56 (25.9 bits)