RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15277
(269 letters)
>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 = 46.8 bits (111), Expect = 8e-07
Identities = 31/133 (23%), Positives = 50/133 (37%), Gaps = 18/133 (13%)
Query: 9 VVCFSDGS--KTPNSTSCAYSI---DKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPH 63
++DGS ++ + I + L S AEL+A+ + LK
Sbjct: 24 YTWYTDGSSFLQEGQRRAGAAVTTETEVIWARALPAGTSAQRAELIAL---TQALKMAEG 80
Query: 64 NKFIIISDSMSALQAISNLNSNNSLVPKIYSHW---LDLKSCGKNLCFLWCPSHCG---- 116
K + +DS A A ++++S + K + L K L + CP H
Sbjct: 81 KKLNVYTDSRYAF-ATAHVHSEGREI-KNKNEILALLKALFLPKRLSIIHCPGHQKGNSA 138
Query: 117 -IKGNESVDNAAR 128
+GN D AAR
Sbjct: 139 EARGNRMADQAAR 151
>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 = 48.9 bits (116), Expect = 9e-07
Identities = 47/299 (15%), Positives = 79/299 (26%), Gaps = 124/299 (41%)
Query: 45 SAELMAIL-------LCIKNLKFL-----PHNKFIIISDSMSALQAISNLNSNNSLVPKI 92
+A+L+AI + L+ L +I + + +S L K+
Sbjct: 153 NAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKF----SAETLSELIRTTLDAEKV 208
Query: 93 YSHWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAARNP---------------------N 131
++ L++ W ++N + P +
Sbjct: 209 FTQGLNILE--------W------------LENPSNTPDKDYLLSIPISCPLIGVIQLAH 248
Query: 132 YNTTLRK--CTSDDFRPIIS--TIIMKNWQT--------SWDNITNNKLKNIK------- 172
Y T + T + R + T + T SW++ + K I
Sbjct: 249 YVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGV 308
Query: 173 ------PKIEEWVSSNRDSRYEE-------IVITRL-------RIGHTR--LTHEF---- 206
P S DS + I+ L + T L
Sbjct: 309 RCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI 368
Query: 207 -LFNKTPRPSCSCGEPLSVQHL------LSCPSH-DQAR----SR--------LP-SVP 244
L N + G P S+ L PS DQ+R R LP + P
Sbjct: 369 SLVN-GAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASP 426
Score = 34.6 bits (79), Expect = 0.034
Identities = 35/218 (16%), Positives = 50/218 (22%), Gaps = 115/218 (52%)
Query: 7 DSVVCFSDGSKTPNSTSCAYSI----DKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLP 62
DS+ + P S SI +Q+ + +NK N LP
Sbjct: 326 DSL---ENNEGVP---SPMLSISNLTQEQVQDY-VNKTN-----------------SHLP 361
Query: 63 HNKFIIISDSMSALQAISNLNSNNSLV--------------------------------- 89
K + IS +N +LV
Sbjct: 362 AGKQV----------EISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSE 411
Query: 90 --PKIY-----------SHWL---------DLKSCGKNLCFLWCPSHCGIKGNESVDNAA 127
K SH L DL + I
Sbjct: 412 RKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNN----VSFNAKDIQI---------- 457
Query: 128 RNPNYNTT----LRKCTSDDFRPIISTIIMK--NWQTS 159
P Y+T LR + I+ II W+T+
Sbjct: 458 --PVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETT 493
Score = 32.3 bits (73), Expect = 0.17
Identities = 15/57 (26%), Positives = 19/57 (33%), Gaps = 20/57 (35%)
Query: 193 TR-LRIGHTRLTHEFL---------------FNKT-PRPSCSCG---EPLSVQHLLS 229
TR L + H L H L FNK P P+ EP + L+
Sbjct: 6 TRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVG 62
Score = 28.1 bits (62), Expect = 3.5
Identities = 7/27 (25%), Positives = 13/27 (48%), Gaps = 3/27 (11%)
Query: 67 IIISDSMSALQAISN-LNSNNSLVPKI 92
+ + + AL ++N LN + KI
Sbjct: 1853 YVAAGDLRALDTVTNVLNFIK--LQKI 1877
>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 = 44.7 bits (106), Expect = 4e-06
Identities = 23/138 (16%), Positives = 41/138 (29%), Gaps = 16/138 (11%)
Query: 1 MNSKYLDSVVCFSDGSKTPNSTSCAYSI---DKQIHSFNL------NKVNSVFSAELMAI 51
M+ + ++DGS + AY+ K + + E+ A
Sbjct: 1 MDDR--TEYDVYTDGSYVNGQYAWAYAFVKDGKVHYEDADVGKNPAAATMRNVAGEIAAA 58
Query: 52 LLCIKNLKFLPHNKFIIISDSMSALQAISNL-NSNNSLVPKIYSHWLDLKSCGKNLCFLW 110
L +K L K I+ D + + N + F
Sbjct: 59 LYAVKKASQLGV-KIRILHDYAGIAFWATGEWKAKNEFTQAYAKLMNQYR---GIYSFEK 114
Query: 111 CPSHCGIKGNESVDNAAR 128
+H G + N+ VD A+
Sbjct: 115 VKAHSGNEFNDYVDMKAK 132
>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 = 41.8 bits (97), Expect = 2e-04
Identities = 45/288 (15%), Positives = 90/288 (31%), Gaps = 75/288 (26%)
Query: 12 FSDGSKTPNSTSCAYSIDKQIHSFNLNKV---NSVFSAELMAILLCIKNLKFLPHNKFII 68
+ P+ + Y I+++ +N N+V +V + L + L L K ++
Sbjct: 98 IKTEQRQPSMMTRMY-IEQRDRLYNDNQVFAKYNVSRLQPYLKL--RQALLELRPAKNVL 154
Query: 69 ISDSMS-------ALQAISNLNSNNSLVPKIYSHWLDLKSCGK---------NLCFLWCP 112
I D + AL + + KI+ WL+LK+C L + P
Sbjct: 155 I-DGVLGSGKTWVALDVCLSYKVQCKMDFKIF--WLNLKNCNSPETVLEMLQKLLYQIDP 211
Query: 113 SHCGIKGNESVDNAARNPNYNTTLRKCTSDDFRPIISTIIM-KNWQTSW---DNITNNK- 167
+ D+++ + + ++ K ++ N+ N K
Sbjct: 212 NWT-----SRSDHSSNIKL--------RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA 258
Query: 168 LK--NIKPKIEEWVSSNRDSRYEEIVITRLR-----IGHTRLTHEFLFNKTPRPSCSCGE 220
N+ KI ++ TR + + TH L + + E
Sbjct: 259 WNAFNLSCKI--------------LLTTRFKQVTDFLSAATTTHISL--DHHSMTLTPDE 302
Query: 221 PLSVQHL-LSCPSHD---QARSRLPSVPALI-----NDPINIDSTLSY 259
S+ L C D + + P ++I + D+
Sbjct: 303 VKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV 350
Score = 37.1 bits (85), Expect = 0.005
Identities = 44/268 (16%), Positives = 82/268 (30%), Gaps = 87/268 (32%)
Query: 4 KYLDSVVCFSDGSKTPNSTSCAY----------SIDKQIHSFNL-NKVNSVFSAELMAIL 52
K D + F + P + ++H ++L K + + +I
Sbjct: 373 KMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIY 432
Query: 53 LCIK----NLKFLPHNKFIIISDSMSALQAISNLNSNNSLVPKI--YSHWLDLKSCGKNL 106
L +K N L H + +S++ + P + Y +
Sbjct: 433 LELKVKLENEYAL-HRSIV------DHYNIPKTFDSDDLIPPYLDQYFYS---------- 475
Query: 107 CFLWCPSHCG--IKGNESVDNAARNPN-YNTTLRKCTSDDFRPIISTIIMKNWQTSWDNI 163
H G +K E + + L DFR + I ++ T+W+
Sbjct: 476 -------HIGHHLKNIEHPERMTLFRMVF---L------DFRFLEQKI--RHDSTAWNAS 517
Query: 164 T--NNKLKNIKPKIEEWVSSNRDSRYEEIVITRLRIGHTRLTHEFLFNKTPRPSCSCGEP 221
N L+ +K + ++ N D +YE +V L +FL E
Sbjct: 518 GSILNTLQQLK-FYKPYICDN-DPKYERLVNAIL---------DFLPK--------IEE- 557
Query: 222 LSVQHLLSCPSHDQARSRLPSVPALIND 249
+L+ D R AL+ +
Sbjct: 558 ----NLICSKYTDLLRI------ALMAE 575
Score = 31.7 bits (71), Expect = 0.31
Identities = 9/54 (16%), Positives = 23/54 (42%), Gaps = 7/54 (12%)
Query: 146 PIISTII---MKNWQTSWDN---ITNNKLKN-IKPKIEEWVSSNRDSRYEEIVI 192
P +II +++ +WDN + +KL I+ + + ++ + +
Sbjct: 327 PRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380
>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 = 41.7 bits (98), Expect = 2e-04
Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 12/82 (14%)
Query: 46 AELMAILLCIKNLKFLPHNKFIIISDSMSALQAISNL--NSNNSLVPKIYSHWLDLKSCG 103
EL AI L +++ + I++DS AL I S + LV +I +
Sbjct: 479 TELQAIYLALQDSG----LEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLI-----K 529
Query: 104 KNLCFL-WCPSHCGIKGNESVD 124
K +L W P+H GI GNE VD
Sbjct: 530 KEKVYLAWVPAHKGIGGNEQVD 551
>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 = 38.9 bits (91), Expect = 0.001
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 12/82 (14%)
Query: 46 AELMAILLCIKNLKFLPHNKFIIISDSMSALQAISN--LNSNNSLVPKIYSHWLDLKSCG 103
AEL A + + + K II DS + +++ S + +V +I +
Sbjct: 476 AELEAFAMALTDSG----PKVNIIVDSQYVMGIVASQPTESESKIVNQIIEEMI-----K 526
Query: 104 KNLCFL-WCPSHCGIKGNESVD 124
K ++ W P+H GI GN+ VD
Sbjct: 527 KEAIYVAWVPAHKGIGGNQEVD 548
>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
sapiens} PDB: 2qk9_A 2qkk_A*
Length = 154
Score = 35.2 bits (82), Expect = 0.008
Identities = 24/96 (25%), Positives = 39/96 (40%), Gaps = 13/96 (13%)
Query: 46 AELMAILLCIKNLKFLPHNKFIIISDSMSALQAISN----------LNSNNSLVPKIYSH 95
AE+ A I+ K NK ++ ++SM + I+N S V
Sbjct: 53 AEIHAACKAIEQAKTQNINKLVLYTNSMFTINGITNWVQGWKKNGWKTSAGKEV-INKED 111
Query: 96 W--LDLKSCGKNLCFLWCPSHCGIKGNESVDNAARN 129
+ L+ + G ++ ++ P H G GNE D AR
Sbjct: 112 FVALERLTQGMDIQWMHVPGHSGFIGNEEADRLARE 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 = 34.5 bits (80), Expect = 0.013
Identities = 25/100 (25%), Positives = 36/100 (36%), Gaps = 24/100 (24%)
Query: 46 AELMAILLCIKNLKFLPHNKFIIISDSMSALQAISN------LN----------SNNSLV 89
EL AI L+ + I++DS AL I+ N LV
Sbjct: 52 TELQAI---YLALQDSGL-EVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLV 107
Query: 90 PKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAARN 129
+I ++ + + W P+H GI GNE VD
Sbjct: 108 NQI----IEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA 143
>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 = 31.5 bits (70), Expect = 0.14
Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 11/36 (30%)
Query: 220 EPLSVQHLLSCPSHDQARSRL--P-SVPAL-INDPI 251
E +++ L QA +L S PAL I +
Sbjct: 18 EKQALKKL-------QASLKLYADDSAPALAIKATM 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 = 28.2 bits (64), Expect = 1.6
Identities = 27/102 (26%), Positives = 37/102 (36%), Gaps = 21/102 (20%)
Query: 47 ELMAILLCIKNLKFLPHNKFIII-SDSMSALQAISN----------LNSNNSLVPKIYSH 95
ELMA I L+ L + +I+ +DS Q I+ ++ V K
Sbjct: 48 ELMA---AIVALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPV-KNVDL 103
Query: 96 W--LDLKSCGKNLCFLWCPSHCGIKGNESVD----NAARNPN 131
W LD + + W H G NE D AA NP
Sbjct: 104 WQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPT 145
>1ytm_A Phosphoenolpyruvate carboxykinase [ATP], phosphoenolpyruvate;
domain closure, nucleotide binding; HET: ATP; 2.20A
{Anaerobiospirillum succiniciproducens} PDB: 1yvy_A
Length = 532
Score = 28.1 bits (63), Expect = 3.3
Identities = 9/23 (39%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 7 DSVVCFSDGSKTPNSTSCAYSID 29
+ V F+D S T N T +Y I
Sbjct: 312 NGKVDFADKSVTEN-TRVSYPIF 333
>2olr_A Phosphoenolpyruvate carboxykinase; carbon dioxide, lyase; HET: ATP;
1.60A {Escherichia coli K12} SCOP: c.91.1.1 c.109.1.1
PDB: 1k3c_A* 1k3d_A* 1aq2_A* 2olq_A* 1os1_A* 2pxz_X*
1ayl_A* 2py7_X* 1oen_A 1ylh_A* 1ygg_A*
Length = 540
Score = 27.8 bits (62), Expect = 4.3
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 7 DSVVCFSDGSKTPNSTSCAYSID 29
D + F DGSKT N T +Y I
Sbjct: 318 DGTIDFDDGSKTEN-TRVSYPIY 339
>1ii2_A Phosphoenolpyruvate carboxykinase; phosphate binding loop, lyase;
2.00A {Trypanosoma cruzi} SCOP: c.91.1.1 c.109.1.1
Length = 524
Score = 27.7 bits (62), Expect = 4.9
Identities = 7/23 (30%), Positives = 9/23 (39%), Gaps = 1/23 (4%)
Query: 7 DSVVCFSDGSKTPNSTSCAYSID 29
+ F D S N T AY +
Sbjct: 291 TGEIDFYDESICKN-TRVAYPLS 312
>1j3b_A ATP-dependent phosphoenolpyruvate carboxykinase; adenosine
triphosphate, T thermophilus; 2.00A {Thermus
thermophilus} SCOP: c.91.1.1 c.109.1.1 PDB: 1xkv_A*
2pc9_A*
Length = 529
Score = 26.9 bits (60), Expect = 8.6
Identities = 9/21 (42%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 9 VVCFSDGSKTPNSTSCAYSID 29
V + D SKT N T +Y I
Sbjct: 306 RVQWDDDSKTEN-TRSSYPIA 325
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 0.132 0.409
Gapped
Lambda K H
0.267 0.0507 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,884,543
Number of extensions: 209204
Number of successful extensions: 345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 343
Number of HSP's successfully gapped: 27
Length of query: 269
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 177
Effective length of database: 4,133,061
Effective search space: 731551797
Effective search space used: 731551797
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)