RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2243
(405 letters)
>2gmh_A Electron transfer flavoprotein-ubiquinone oxidoreductase; HET: BHG
FAD UQ5; 2.50A {Sus scrofa} SCOP: c.3.1.2 d.16.1.8
d.58.1.6 PDB: 2gmj_A*
Length = 584
Score = 152 bits (385), Expect = 4e-41
Identities = 62/80 (77%), Positives = 69/80 (86%)
Query: 291 TPKPQKGDNTFLKPASECKPIEYPKPDGQVSFDLLSSVALTGTNHEGDQPAHLTLKDDSV 350
T K + D+ LKPA +C PIEYPKPDGQ+SFDLLSSVAL+GTNHE DQPAHLTLKDDSV
Sbjct: 452 TLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTLKDDSV 511
Query: 351 PVNTNLAVYDGPEGRFCPAG 370
PVN NL++YDGPE RFCPAG
Sbjct: 512 PVNRNLSIYDGPEQRFCPAG 531
>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 = 54.7 bits (132), Expect = 2e-09
Identities = 31/152 (20%), Positives = 51/152 (33%), Gaps = 21/152 (13%)
Query: 139 MNENYGDFVQVYTDGSKSDSSVGCAFVIPQLHIVKKQ-------TLNPKSSIFHAELLAI 191
M++ VYTDGS + A+ + V + E+ A
Sbjct: 1 MDDR--TEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAA 58
Query: 192 SDAVSTIKSQSIGEAVIISDSLSALQAISSMSH-----SNPLVQSIHEEISTIPNSTIKF 246
AV + + I+ D I+ + N Q+ + ++ F
Sbjct: 59 LYAVKKASQLGV-KIRILHDY----AGIAFWATGEWKAKNEFTQAYAKLMNQY-RGIYSF 112
Query: 247 FWCPSHVGIAGNDAADLEAKSALENP-ISHDH 277
+H G ND D++AKSAL + H H
Sbjct: 113 EKVKAHSGNEFNDYVDMKAKSALGIRDLEHHH 144
>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 = 53.3 bits (128), Expect = 1e-08
Identities = 27/142 (19%), Positives = 48/142 (33%), Gaps = 20/142 (14%)
Query: 149 VYTDGSKSDSS----VGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIG 204
YTDGS G A ++ + L +S AEL+A++ A+ + + +
Sbjct: 26 WYTDGSSFLQEGQRRAGAAVTTET-EVIWARALPAGTSAQRAELIALTQALKMAEGKKL- 83
Query: 205 EAVIISDSLSALQAISSMSHSNP-----LVQSIHEEISTIPNSTIKFFWCPSHVG----- 254
+ +DS A S + ++ + + + CP H
Sbjct: 84 --NVYTDSRYAFATAHVHSEGREIKNKNEILALLKALFLPKR--LSIIHCPGHQKGNSAE 139
Query: 255 IAGNDAADLEAKSALENPISHD 276
GN AD A+ A +
Sbjct: 140 ARGNRMADQAAREAAMKAVLET 161
>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 = 52.7 bits (126), Expect = 1e-07
Identities = 78/479 (16%), Positives = 139/479 (29%), Gaps = 152/479 (31%)
Query: 7 NQCLRLATGAFRS---------SPTASLEAETSEPNLKIRRSILTCNYIAKVMHHNSTNP 57
+Q L L F + + A L E +K + ++ A++M + P
Sbjct: 81 DQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVK-TKELIKNYITARIM---AKRP 136
Query: 58 NFKRINNPPYKVLYENSTKLNPTVGIQ----------REI------LMND-IPFHKVILQ 100
K+ N+ ++ + E + +L G Q R++ L+ D I F L
Sbjct: 137 FDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLS 196
Query: 101 REPKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTD-GSKSDSS 159
+ + +VF Q + ++ + + D
Sbjct: 197 ELIRTT-----LDAE-------------KVFTQGL---------NILEWLENPSNTPDKD 229
Query: 160 --VGCAFVIP-----QL-HIV---KKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVI 208
+ P QL H V K P EL + + SQ + AV
Sbjct: 230 YLLSIPISCPLIGVIQLAHYVVTAKLLGFTP------GELRSYLKGATGH-SQGLVTAVA 282
Query: 209 ISDSLS-------ALQAISSMSHSNPLVQSIHEE--ISTIPNSTIKFFW-----CPSH-V 253
I+++ S +AI+ + V+ +E +++P S ++ PS +
Sbjct: 283 IAETDSWESFFVSVRKAITVLFFIG--VRC-YEAYPNTSLPPSILEDSLENNEGVPSPML 339
Query: 254 GIAGNDAADLEAKSALEN---PISHDHGIGLTQ------LSG----LFA-----HTPKPQ 295
I+ ++ N P I L +SG L+ K
Sbjct: 340 SISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAP 399
Query: 296 KGDNTFLKPASECKPIEYPKPDGQVSF---------DLLSSVALTGTNHEGDQPAHLTLK 346
G + P SE K F LL + K
Sbjct: 400 SGLDQSRIPFSE------RKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAK 453
Query: 347 DDSVPV-NTNLAVYDGPEGRFCPAGKLENHNTQNYVESLGPKNDNRTLKSLYITL--NW 402
D +PV +T +DG + + S+ + + I L W
Sbjct: 454 DIQIPVYDT----FDG-------------SDLRVLSGSISER-----IVDCIIRLPVKW 490
Score = 48.1 bits (114), Expect = 4e-06
Identities = 44/290 (15%), Positives = 82/290 (28%), Gaps = 115/290 (39%)
Query: 70 LYENSTKLNPTVGIQREI-------LMNDIPFHKV-ILQREPKESWLHKKPSCNLSLTLY 121
LY+ S +++ + F + I+ P LT++
Sbjct: 1635 LYKTS----KAA---QDVWNRADNHFKDTYGFSILDIVINNPVN------------LTIH 1675
Query: 122 KKDGMPHQVFQQEFQRNMNENYGDFV-QVYTDGSK---------SDSSVGCAFVIP---- 167
F E + + ENY + + DG ++ S F
Sbjct: 1676 ---------FGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLL 1726
Query: 168 ------Q----------LHIVKKQTLNPKSSIF--H-----------AELLAISDAVSTI 198
Q +K + L P + F H A++++I V +
Sbjct: 1727 SATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVV 1786
Query: 199 KS--QSIGEAV---IISDSLSALQAI--SSMSHSNPL--VQSIHEEIST----------- 238
++ AV + S + AI ++ S +Q + E +
Sbjct: 1787 FYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLVEIVNY 1846
Query: 239 -IPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPISHD--HGIGLTQLS 285
+ N V AG DL A + N ++ I + +L
Sbjct: 1847 NVENQQY--------V-AAG----DLRALDTVTNVLNFIKLQKIDIIELQ 1883
Score = 38.1 bits (88), Expect = 0.006
Identities = 75/406 (18%), Positives = 125/406 (30%), Gaps = 148/406 (36%)
Query: 94 FHKVILQREPKESWLHKKPSCNLSLTLY-----------KKDGMPHQVFQ---QEFQRN- 138
F+K IL + +P+ L K G QV EF+
Sbjct: 37 FNK-ILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCY 95
Query: 139 MNENYGD---FVQVYTDGSKSDSSVGCAFVIPQ-----LHIVKKQTLNPKSSIFHAELLA 190
+ N D ++D+++ + + + K+ +S A
Sbjct: 96 LEGN--DIHALAAKLL--QENDTTLVKTKELIKNYITARIMAKRPFDKKSNS-------A 144
Query: 191 ISDAVSTIKSQSIGEAVIIS---------DSLSALQAISSMSHS--NPLVQSIHE---EI 236
+ AV G A +++ D L+ + H L++ E E+
Sbjct: 145 LFRAVGE------GNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSEL 198
Query: 237 STIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENPIS-HDH-----------GIGLTQL 284
K F + G+ ++ LENP + D IG+ QL
Sbjct: 199 IRTTLDAEKVF---TQ-GL------NI--LEWLENPSNTPDKDYLLSIPISCPLIGVIQL 246
Query: 285 SGLFAH----------TPKPQKGD-NTFLKPASECKPIEYPKPDGQV------------S 321
AH TP G+ ++LK A+ G V S
Sbjct: 247 ----AHYVVTAKLLGFTP----GELRSYLKGATGHS-------QGLVTAVAIAETDSWES 291
Query: 322 FDLLSSVALT-----GTN-HEGDQPAHLTLK--DDSVPVNTN-----LAVYDGPE----- 363
F + A+T G +E L +DS+ N L++ + +
Sbjct: 292 FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQD 351
Query: 364 --GRFC---PAGK---LENHNT-QNYVESLGPKNDNRTLKSLYITL 400
+ PAGK + N +N V S GP ++L L +TL
Sbjct: 352 YVNKTNSHLPAGKQVEISLVNGAKNLVVS-GPP---QSLYGLNLTL 393
Score = 36.2 bits (83), Expect = 0.024
Identities = 51/322 (15%), Positives = 81/322 (25%), Gaps = 152/322 (47%)
Query: 10 LRLATGAF-RSSPTASLEAETSE-------PNLKIR---RSILTCNYIAKVMHHNSTNPN 58
+R A+ +S S+ ++ E P L I + + Y+ K NS P
Sbjct: 308 VR-CYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQD-YVNKT---NSHLPA 362
Query: 59 FKRI-----NNP-------PYKVLYENSTKL----NPTVGIQREILMNDIPFHKVILQRE 102
K++ N P + LY + L P+ Q I PF +R
Sbjct: 363 GKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRI-----PFS----ER- 412
Query: 103 PKESWLHKKPSCNLSLTLYKKDGMPHQVFQQEFQRNMNENYGDFVQVYTDGSKSDSSVGC 162
K F F
Sbjct: 413 --------KL-----------------KFSNRF--------------------------- 420
Query: 163 AFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVIIS-DSL-------- 213
L P +S FH+ LL A I + V + +
Sbjct: 421 --------------L-PVASPFHSHLLV--PASDLINKDLVKNNVSFNAKDIQIPVYDTF 463
Query: 214 --SALQAISSMSHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALEN 271
S L+ S + + I + I +P W ++ +
Sbjct: 464 DGSDLR-----VLSGSISERIVDCIIRLP-----VKW-----------------ETTTQF 496
Query: 272 PISH--DHGIG-LTQLSGLFAH 290
+H D G G + L L
Sbjct: 497 KATHILDFGPGGASGLGVLTHR 518
Score = 28.5 bits (63), Expect = 6.1
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 21/75 (28%)
Query: 272 PISHDHGIGLTQLSGLFAHT-PKPQKG---DNTFLKPASECKPIE-----------YPKP 316
+ +QL F P+P +G D+ +P + P E +P
Sbjct: 21 LVPTASFFIASQLQEQFNKILPEPTEGFAADD---EPTT---PAELVGKFLGYVSSLVEP 74
Query: 317 DGQVSFDLLSSVALT 331
FD + ++ LT
Sbjct: 75 SKVGQFDQVLNLCLT 89
>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 = 50.6 bits (120), Expect = 7e-07
Identities = 56/346 (16%), Positives = 98/346 (28%), Gaps = 119/346 (34%)
Query: 2 LDPVQN---------QCLRLATGAFRS----------------------SPTASLE---- 26
L VQN C L T F+ +P
Sbjct: 250 LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLK 309
Query: 27 ----AETSEPNLKIRRSILTCNYIAKVMH-HNSTNPNFKRINNPPYKVLYENS-TKLNPT 80
P + + + IA+ + +T N+K +N + E+S L P
Sbjct: 310 YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA 369
Query: 81 VGIQRE------ILMND--IP----------------------FHKV-ILQREPKES--- 106
R+ + IP HK +++++PKES
Sbjct: 370 --EYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS 427
Query: 107 ----------------WLHKK--PSCNLSLTLYKKDGMPHQVFQQEFQ--------RNMN 140
LH+ N+ T D +P + Q +
Sbjct: 428 IPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHP 487
Query: 141 ENYGDFVQVYTD----GSK----SDSSVGCAFVIPQLHIVK--KQTLNPKSSIFHAELLA 190
E F V+ D K S + ++ L +K K + + + A
Sbjct: 488 ERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNA 547
Query: 191 ISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEI 236
I D + I E +I S L+ I+ M+ + + H+++
Sbjct: 548 ILDFL-----PKIEENLICSKYTDLLR-IALMAEDEAIFEEAHKQV 587
Score = 41.4 bits (96), Expect = 5e-04
Identities = 52/347 (14%), Positives = 94/347 (27%), Gaps = 101/347 (29%)
Query: 23 ASLEAETSEPNLKIRRSILTCNYIAKVMHHNSTNPNFKRINNP---PYKVLYENSTKLNP 79
+ ++ E +P S++T YI + + N F + N PY L + +L P
Sbjct: 96 SPIKTEQRQP------SMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRP 149
Query: 80 ----TV----GIQREILMND-IPFHKVILQREPKESWLH----KKPSC------NLSLTL 120
+ G + + D +KV + + K WL+ P L +
Sbjct: 150 AKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209
Query: 121 YKK-----DGM---PHQV--FQQEFQRNM-NENYG------DFVQ------VYTDGSK-- 155
D ++ Q E +R + ++ Y VQ + K
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL 269
Query: 156 ---SDSSVGCAFVIPQLHIVKKQTLNPKSSIF-HAELLAISDAVSTIKSQS--------- 202
V + +L+ S E+ ++ + Q
Sbjct: 270 LTTRFKQV--TDFLSAAT-TTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN 326
Query: 203 ------IGEAV--------------------IISDSLSALQAISSMSHSNPLVQSIHEEI 236
I E++ II SL+ L+ + L S+
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRL--SVFPPS 384
Query: 237 STIPNSTIKFFWCPSHVGIAGNDAADLEAKSALE----NPISHDHGI 279
+ IP + W L S +E I
Sbjct: 385 AHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI 431
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 44.9 bits (107), Expect = 7e-06
Identities = 33/159 (20%), Positives = 56/159 (35%), Gaps = 41/159 (25%)
Query: 144 GDFVQVYTDGSKSDSS-----VGCAFVIPQLHIVKKQTLNPKSSIFH---------AELL 189
GDFV VYTDG S A + V +P + AE+
Sbjct: 5 GDFVVVYTDGC---CSSNGRRRPRAGIG-----VYWGPGHPLNVGIRLPGRQTNQRAEIH 56
Query: 190 AISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHS---------------NP-LVQSIH 233
A A+ K+Q+I + V+ ++S+ + I++ N ++
Sbjct: 57 AACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALE 116
Query: 234 EEISTIPNSTIKFFWCPSHVGIAGNDAADLEAKSALENP 272
+ I++ P H G GN+ AD A+ +
Sbjct: 117 RLTQGM---DIQWMHVPGHSGFIGNEEADRLAREGAKQS 152
>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 = 41.3 bits (97), Expect = 4e-04
Identities = 34/120 (28%), Positives = 53/120 (44%), Gaps = 18/120 (15%)
Query: 150 YTDGSKS-DSSVGCAFVIP----QLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIG 204
Y DG+ + ++ +G A + Q + T N K+ + A LA+ D S
Sbjct: 443 YVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTEL-QAIYLALQD--------SGL 493
Query: 205 EAVIISDSLSALQAISSM--SHSNPLVQSIHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
E I++DS AL I + + LV I E++ I + W P+H GI GN+ D
Sbjct: 494 EVNIVTDSQYALGIIQAQPDKSESELVNQIIEQL--IKKEKVYLAWVPAHKGIGGNEQVD 551
>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 = 38.7 bits (91), Expect = 8e-04
Identities = 36/148 (24%), Positives = 54/148 (36%), Gaps = 32/148 (21%)
Query: 147 VQVYTDGS-KSDSSVG-CAFVIP---QLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQ 201
Y DG+ ++ +G +V Q + T N K EL AI A+
Sbjct: 13 ETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQK-----TELQAIYLALQDSGL- 66
Query: 202 SIGEAVIISDSLSALQAISSMSH---------------SN-PLVQSIHEEISTIPNSTIK 245
E I++DS AL I+ H N LV I E++ I +
Sbjct: 67 ---EVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQL--IKKEKVY 121
Query: 246 FFWCPSHVGIAGNDAADLEAKSALENPI 273
W P+H GI GN+ D + + +
Sbjct: 122 LAWVPAHKGIGGNEQVDKLVSAGIRKVL 149
>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 = 39.3 bits (92), Expect = 0.002
Identities = 29/91 (31%), Positives = 39/91 (42%), Gaps = 15/91 (16%)
Query: 175 QTLNPKSSIFHAELLAISDAVSTIKSQSIGEAV-IISDSLSALQAISSM--SHSNPLVQS 231
QT N + AEL A + A+ G V II DS + ++S + +V
Sbjct: 470 QTTNQQ-----AELEAFAMAL-----TDSGPKVNIIVDSQYVMGIVASQPTESESKIVNQ 519
Query: 232 IHEEISTIPNSTIKFFWCPSHVGIAGNDAAD 262
I EE+ I I W P+H GI GN D
Sbjct: 520 IIEEM--IKKEAIYVAWVPAHKGIGGNQEVD 548
>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 = 34.4 bits (80), Expect = 0.022
Identities = 14/36 (38%), Positives = 18/36 (50%)
Query: 243 TIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHG 278
IK+ W H G N+ AD A++A NP D G
Sbjct: 115 QIKWEWVKGHAGHPENERADELARAAAMNPTLEDTG 150
>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
{Shewanella oneidensis} PDB: 2zqb_A
Length = 158
Score = 30.6 bits (70), Expect = 0.49
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 243 TIKFFWCPSHVGIAGNDAADLEAKSALE-NPISHDHG 278
I + W H G A N+ D A++A E NP D G
Sbjct: 117 QIDWRWVKGHAGHAENERCDQLARAAAEANPTQIDTG 153
>2ctz_A O-acetyl-L-homoserine sulfhydrylase; crystal, O-acetyl homoserine
sulfhydrase, structural genomic structural
genomics/proteomics initiative; HET: PLP; 2.60A {Thermus
thermophilus} SCOP: c.67.1.3
Length = 421
Score = 31.3 bits (72), Expect = 0.55
Identities = 10/57 (17%), Positives = 18/57 (31%), Gaps = 18/57 (31%)
Query: 257 GNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFLKPASECKPIEY 313
+ DLEA + + + G+ DNTF +P+ +
Sbjct: 157 ALNIPDLEALAQ----AAREKGV--------------ALIVDNTFGMGGYLLRPLAW 195
>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 = 31.4 bits (71), Expect = 0.60
Identities = 11/84 (13%), Positives = 26/84 (30%), Gaps = 5/84 (5%)
Query: 23 ASLEAETSEPNLKIR--RSILTCNYIAKVMHHNSTNPNFKRINNPPYKVLYENSTKLNPT 80
++ + + R + M +N F + PY E L+P
Sbjct: 1464 GAITEDRYNEYVAKVSAREKSAYKFFHNGMIYNKL---FVSKEHAPYTDELEEDVYLDPL 1520
Query: 81 VGIQREILMNDIPFHKVILQREPK 104
+ ++ + F+ +Q +
Sbjct: 1521 ARVSKDKKSGSLTFNSKNIQSKDS 1544
Score = 28.7 bits (64), Expect = 4.3
Identities = 9/29 (31%), Positives = 12/29 (41%), Gaps = 8/29 (27%)
Query: 250 PSHV--------GIAGNDAADLEAKSALE 270
P+ V G G D E+K +LE
Sbjct: 620 PAQVILPMSPNHGTFGGDGMYSESKLSLE 648
>3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease,
hydrolase, magnesium, metal-binding; 1.60A
{Chlorobaculum tepidum}
Length = 146
Score = 30.1 bits (69), Expect = 0.64
Identities = 7/30 (23%), Positives = 11/30 (36%)
Query: 243 TIKFFWCPSHVGIAGNDAADLEAKSALENP 272
+ F H N AD A+ A++
Sbjct: 116 RVTFHKVKGHSDNPYNSRADELARLAIKEN 145
>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 = 0.74
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 4/24 (16%)
Query: 104 KESWLHKKPSCNLSLTLYKKDGMP 127
K++ L K + SL LY D P
Sbjct: 19 KQA-LKKLQA---SLKLYADDSAP 38
Score = 28.4 bits (62), Expect = 2.4
Identities = 8/21 (38%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 22 TASLE--AETSEPNLKIRRSI 40
ASL+ A+ S P L I+ ++
Sbjct: 26 QASLKLYADDSAPALAIKATM 46
>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
Length = 166
Score = 29.5 bits (67), Expect = 1.0
Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 16/63 (25%)
Query: 243 TIKFFWCPSHVGIAGNDAADLEAKSALENPISHDHGIGLTQLSGLFAHTPKPQKGDNTFL 302
++F + H G N+ D EA+ ++ A TP P + F
Sbjct: 120 RVRFHFVKGHTGHPENERVDREARRQAQSQ----------------AKTPCPPRAPTLFH 163
Query: 303 KPA 305
+ A
Sbjct: 164 EEA 166
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 0.131 0.387
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: 5,757,561
Number of extensions: 325743
Number of successful extensions: 410
Number of sequences better than 10.0: 1
Number of HSP's gapped: 405
Number of HSP's successfully gapped: 26
Length of query: 405
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 309
Effective length of database: 4,021,377
Effective search space: 1242605493
Effective search space used: 1242605493
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (26.0 bits)