RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8376
(328 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 = 50.4 bits (121), Expect = 5e-08
Identities = 22/143 (15%), Positives = 44/143 (30%), Gaps = 17/143 (11%)
Query: 54 DNKDKILCYTDGS-KTNTFTGGAYLLNETVEQFQLNQIASIYT--------AELMAIDLC 104
D++ + YTDGS + + + ++ + E+ A
Sbjct: 2 DDRTEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAA--- 58
Query: 105 LNSILMYIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFL 164
L ++ Q I D ++ K+ + SF
Sbjct: 59 LYAVKKASQLG---VKIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMN--QYRGIYSFE 113
Query: 165 WIPSHVGIRENEMVDRAARNAVN 187
+ +H G N+ VD A++A+
Sbjct: 114 KVKAHSGNEFNDYVDMKAKSALG 136
>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 = 49.8 bits (119), Expect = 1e-07
Identities = 31/136 (22%), Positives = 47/136 (34%), Gaps = 21/136 (15%)
Query: 62 YTDGS-KTNTFTGGA----YLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNF 116
YTDGS A E + L S AEL+A+ L
Sbjct: 27 YTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIALTQALKMAEG------ 80
Query: 117 CFKDFVICSDSKSSLQAL--KFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVG--- 171
K + +DS+ + + ++IL +K + ++S + P H
Sbjct: 81 --KKLNVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFL-PKRLSIIHCPGHQKGNS 137
Query: 172 --IRENEMVDRAARNA 185
R N M D+AAR A
Sbjct: 138 AEARGNRMADQAAREA 153
>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 = 40.8 bits (95), Expect = 5e-04
Identities = 44/299 (14%), Positives = 83/299 (27%), Gaps = 89/299 (29%)
Query: 78 LNETVEQF-QLNQIASIYTAELMAIDLCLNSILMYIQNNFCFKDFVICSDSKSSLQALKF 136
L E E F ++ + AEL+ L Y+ V S Q L
Sbjct: 41 LPEPTEGFAADDEPTTP--AELVG------KFLGYVS------SLVEPSKVGQFDQVLNL 86
Query: 137 NLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVDRA---ARNAVNARLTNQ 193
L + L+ +I + + L + + + + + + AR +
Sbjct: 87 CLTE---FENCYLEGNDIHAL---AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKK 140
Query: 194 YTSSDYKAHFKHIQFKRWEEIWRQNAVLGRQ---------LRQI----KTDVRKWKSSNR 240
S A F+ + E + A+ G Q LR + V
Sbjct: 141 SNS----ALFRAVG----EGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDL----- 187
Query: 241 NIRQEEVVLCRL---------RIGHCLATHKHLLERKDPPACEFCGQTPV--------YL 283
I+ L L L + L + P ++ P+ L
Sbjct: 188 -IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQL 246
Query: 284 NHWLTECHALG----NLRRQ------HQRSIL-----------QDNVETIDRCMKFLYH 321
H++ LG LR H + ++ + ++ + + L+
Sbjct: 247 AHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFF 305
Score = 37.0 bits (85), Expect = 0.009
Identities = 24/121 (19%), Positives = 38/121 (31%), Gaps = 30/121 (24%)
Query: 1 MDDYKL--EVRCVIKQQKEEPQWLL---------HQPK-VTMLISSKKDEELPSEINNKY 48
MD YK + V + + + P +T+ +K + I Y
Sbjct: 1633 MDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKR----IRENY 1688
Query: 49 LEFKKDNK-------DKILCYTDGSKTN-TFTGGAYLLNETVEQFQLNQIASIYTAELMA 100
+ +KI + T+ TF LL+ T QF Q A + E A
Sbjct: 1689 SAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSAT--QFT--QPA-LTLME-KA 1742
Query: 101 I 101
Sbjct: 1743 A 1743
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 38.7 bits (91), Expect = 7e-04
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 160 QVSFLWIPSHVGIRENEMVDRAARNAVN 187
+ ++ +P H G NE DR AR
Sbjct: 123 DIQWMHVPGHSGFIGNEEADRLAREGAK 150
>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 = 38.3 bits (90), Expect = 7e-04
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 160 QVSFLWIPSHVGIRENEMVDRAARNAV 186
+V W+P+H GI NE VD+ +
Sbjct: 119 KVYLAWVPAHKGIGGNEQVDKLVSAGI 145
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 36.7 bits (86), Expect = 0.003
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 160 QVSFLWIPSHVGIRENEMVDRAARNAVNAR 189
Q+ + W+ H G ENE D+ AR A A
Sbjct: 117 QIDWRWVKGHAGHAENERCDQLARAAAEAN 146
>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 = 36.7 bits (86), Expect = 0.003
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 160 QVSFLWIPSHVGIRENEMVDRAARNAVN 187
Q+ + W+ H G ENE D AR A
Sbjct: 115 QIKWEWVKGHAGHPENERADELARAAAM 142
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 36.8 bits (86), Expect = 0.003
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 160 QVSFLWIPSHVGIRENEMVDRAARNAVNAR 189
+V F ++ H G ENE VDR AR ++
Sbjct: 120 RVRFHFVKGHTGHPENERVDREARRQAQSQ 149
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 36.3 bits (85), Expect = 0.004
Identities = 8/28 (28%), Positives = 12/28 (42%)
Query: 160 QVSFLWIPSHVGIRENEMVDRAARNAVN 187
+V+F + H N D AR A+
Sbjct: 116 RVTFHKVKGHSDNPYNSRADELARLAIK 143
>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 = 36.8 bits (84), Expect = 0.010
Identities = 48/380 (12%), Positives = 122/380 (32%), Gaps = 96/380 (25%)
Query: 6 LEVRCVIKQQKEEPQWLLHQP----KVTMLISSKKDEELPSEINNK--YLEFKKDNKDKI 59
L++R + + + L+ K + + ++ +++ K +L K N +
Sbjct: 138 LKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPET 197
Query: 60 -------LCYTDGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYI 112
L Y + + + + + Q ++ + ++ L L +L+ +
Sbjct: 198 VLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQ-AELRRLLKSKPYENCL-L--VLLNV 253
Query: 113 QNNFCFKDFVI-C-----------SDSKSSLQALKFNLND-----------SILISKILL 149
QN + F + C +D S+ +L+ S+L+ +
Sbjct: 254 QNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC 313
Query: 150 KIKEISSFGSQVSFLWIPSHVGIRENEMVDRAA--RNAVNARLT-------NQYTSSDYK 200
+ +++ + + S + + + ++ +LT N ++Y+
Sbjct: 314 RPQDLPREVLTTNPRRL-SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372
Query: 201 AHFK---------HIQFKRWEEIWRQNAVLGRQLRQI------KTDVRKWKSSNR----N 241
F HI IW V+ + + + V K + +
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIW--FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS 430
Query: 242 IRQEEVVLCRLRIGHCLATHKHLLERKDPPACEFCGQTPV----------YLNHWLTECH 291
I E ++++ + A H+ +++ + P F + ++ H H
Sbjct: 431 IYLEL----KVKLENEYALHRSIVDHYNIPKT-FDSDDLIPPYLDQYFYSHIGH-----H 480
Query: 292 ALGNLRRQHQ----RSILQD 307
L N+ + R + D
Sbjct: 481 -LKNIEHPERMTLFRMVFLD 499
Score = 32.9 bits (74), Expect = 0.16
Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 1/62 (1%)
Query: 5 KLEVRCVIKQQKEEPQWLLHQPKVTMLISSKKDEELPSEINNKYLEFKK-DNKDKILCYT 63
KL ++++Q +E + + + + + + L I + Y K D+ D I Y
Sbjct: 410 KLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL 469
Query: 64 DG 65
D
Sbjct: 470 DQ 471
Score = 29.8 bits (66), Expect = 1.7
Identities = 34/228 (14%), Positives = 66/228 (28%), Gaps = 66/228 (28%)
Query: 16 KEEP----QWL-LHQPKVTMLISSKKDEELPSEINNKYLE---FKKDNK--DKILC--YT 63
++ W ++ K+T +I S + P+E + F +L +
Sbjct: 338 RDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWF 397
Query: 64 DGSKTNTFTGGAYLLNETVEQFQLNQIASIYTAELMAIDLCL-----------NSIL-MY 111
D K++ ++N+ + + + T + +I L L SI+ Y
Sbjct: 398 DVIKSDVMV----VVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHY 453
Query: 112 -IQNNFCFKDFVI-CSDS----------KSSLQALKFNLNDSILISKILLKIKEISSFGS 159
I F D + D K+ + L + L
Sbjct: 454 NIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMT-----LFRMVFL---------- 498
Query: 160 QVSFLWIPSHVGIRENEMVDRAARNAVNARLTNQYTSSDYKAHFKHIQ 207
F ++ + R A NA + T K + +I
Sbjct: 499 --DFRFLEQKI---------RHDSTAWNASGSILNTLQQLKFYKPYIC 535
>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 = 29.9 bits (66), Expect = 0.57
Identities = 9/35 (25%), Positives = 12/35 (34%), Gaps = 9/35 (25%)
Query: 50 EFKK-DNKDKILCYTDGSKTNTFTGGAYLLNETVE 83
KK K+ Y D S A + T+E
Sbjct: 21 ALKKLQASLKL--YADDSAP------ALAIKATME 47
>3u3g_D Ribonuclease H, RNAse H1; hydrolase, cleave the RNA strand of
RNA/DNA hybrid; 1.40A {Uncultured organism}
Length = 140
Score = 29.4 bits (67), Expect = 0.74
Identities = 26/144 (18%), Positives = 55/144 (38%), Gaps = 14/144 (9%)
Query: 57 DKILCYTDG-SKTNTFTG--GAYLLNETVEQF-QLNQIASIYT---AELMAIDLCLNSIL 109
+KI+ YTDG ++ N G + +E + + T AE A+ L +
Sbjct: 2 NKIIIYTDGGARGNPGPAGIGVVITDEKGNTLHESSAYIGETTNNVAEYEALIRALEDLQ 61
Query: 110 MYIQNNFCFKDFVICSDSKSSLQALK--FNLNDSILISKILLKIKEISSFGSQVSFLWIP 167
M+ + + DS+ ++ ++ + + + L + KI I + +
Sbjct: 62 MFGDKL-VDMEVEVRMDSELIVRQMQGVYKVKEPTLK-EKFAKIAHIKM---ERVPNLVF 116
Query: 168 SHVGIRENEMVDRAARNAVNARLT 191
H+ +N D A++ L+
Sbjct: 117 VHIPREKNARADELVNEAIDKALS 140
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 28.6 bits (63), Expect = 1.9
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 3/42 (7%)
Query: 209 KRWEEIWRQNAV--LGRQLRQIKTDVRKWKSSNRNIRQEEVV 248
K E+ WR+ A L ++ V K K +NR +
Sbjct: 106 KVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNRI-ADKAFY 146
>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 = 29.3 bits (66), Expect = 2.1
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 8/43 (18%)
Query: 140 DSILISKIL--LKIKEISSFGSQVSFLWIPSHVGIRENEMVDR 180
+S L+++I+ L KE +V W+P+H GI NE VD+
Sbjct: 516 ESELVNQIIEQLIKKE------KVYLAWVPAHKGIGGNEQVDK 552
>3lqz_A HLA class II histocompatibility antigen, DP alpha; MHC, immune,
disulfide bond, glycoprotein, immune respo membrane, MHC
II, transmembrane, immune system; HET: NAG NDG; 3.25A
{Homo sapiens}
Length = 181
Score = 28.6 bits (64), Expect = 2.3
Identities = 15/98 (15%), Positives = 26/98 (26%), Gaps = 14/98 (14%)
Query: 198 DYKAHFKHIQFKRWEEIWRQNAVLGRQLRQIKTDVRKWKSSNRNIRQEEVVLCRLRIGHC 257
D F ++ + E +W + + S + + +
Sbjct: 27 DEDEMF-YVDLDKKETVWH------------LEEFGQAFSFEAQGGLANIAILNNNLNTL 73
Query: 258 LATHKHLLERKDPPACEFCGQTPVYLNHWLT-ECHALG 294
+ H DPP + PV L T CH
Sbjct: 74 IQRSNHTQATNDPPEVTVFPKEPVELGQPNTLICHIDK 111
>3qcp_A QSOX from trypanosoma brucei (tbqsox); ERV fold, thioredoxin fold,
sulfhydryl oxidase, oxidoreducta; HET: FAD; 2.30A
{Trypanosoma brucei} PDB: 3qd9_A*
Length = 470
Score = 27.7 bits (60), Expect = 6.4
Identities = 12/50 (24%), Positives = 15/50 (30%), Gaps = 11/50 (22%)
Query: 181 AARNAVNARLTNQYTSSDYKAHFKHIQF---------KRWEEIWRQNAVL 221
A N VNARL N +D QF + + V
Sbjct: 359 RAHNNVNARLANVKDGADPL--VPKRQFPTLEACTECYDGAGNFIEAHVT 406
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
0.322 0.135 0.409
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,805,161
Number of extensions: 270084
Number of successful extensions: 535
Number of sequences better than 10.0: 1
Number of HSP's gapped: 531
Number of HSP's successfully gapped: 26
Length of query: 328
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 234
Effective length of database: 4,077,219
Effective search space: 954069246
Effective search space used: 954069246
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: 57 (25.6 bits)