RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= 537021.9.peg.477_1 (235 letters) >gnl|CDD|162493 TIGR01695, mviN, integral membrane protein MviN. This model represents MviN, a family of integral membrane proteins predicted to have ten or more transmembrane regions. Although frequently listed as a virulence protein, it is not restricted to pathogens and it is an essential protein in Sinorhizobium meliloti. In a number of species its gene is adjacent to that of the uridylyltransferase GlnD, the signal-transducing enzyme that performs the key modification to the nitrogen regulatory protein PII. Length = 502 Score = 91.6 bits (228), Expect = 1e-19 Identities = 56/173 (32%), Positives = 97/173 (56%) Query: 1 MAALLPKLSSAIQLENKQQSSELRNRAIEYVLFFGIPCTAILLMLPKEIIQTLYERGAFT 60 LLPKLS N + +L N+ I L IP + LL+L I+ L+ERGAF+ Sbjct: 280 STVLLPKLSRHASEGNWNELRDLLNQGIRLSLLLTIPSSFGLLILSIPIVSLLFERGAFS 339 Query: 61 AQDTILVSSYLSIYSTEIVGFLLSRVLLSEFYARNDVKTPAKFYILSIVMGFVIAIGLFP 120 +DT++ ++ L+ Y ++ + L +VLL FYAR D +TP ++S+V+ ++++ L Sbjct: 340 EEDTVMTATILAAYGLGLIFYSLQKVLLRAFYARKDTRTPFINSVISVVLNALLSLLLIF 399 Query: 121 FIGGYGIATAEVSWVWVNTICLAVALLKRRQIDLPFQTIYRILSIFISSGLMG 173 +G GIA A + V+++ L + L +R + LPF + + + I+S ++G Sbjct: 400 PLGLVGIALATSAASMVSSVLLYLMLNRRLKGILPFGVLKVLAKLVIASAIIG 452 >gnl|CDD|162043 TIGR00797, matE, putative efflux protein, MATE family. The MATE family consists of probable efflux proteins including a functionally characterized multi drug efflux system from Vibrio parahaemolyticus, a putative ethionine resistance protein of Saccharomyces cerevisiae, and the functionally uncharacterized DNA damage-inducible protein F (DinF) of E. coli. These proteins have 12 probable TMS. Length = 342 Score = 35.7 bits (83), Expect = 0.010 Identities = 35/158 (22%), Positives = 64/158 (40%), Gaps = 12/158 (7%) Query: 3 ALLPKLSSAIQLENKQQSSELRNRAIEYVLFFGIPCTAILLMLPKEIIQTLYERGAFTAQ 62 A ++ A+ N Q+ +++ L G+P + ++ A Sbjct: 51 ATTALVAQAVGAGNYQRLGRQAQQSLLLALLLGLPVLLVGYFFIDPLL------SLMGAD 104 Query: 63 DTI--LVSSYLSIYSTEIVGFLLSRVLLSEFYARNDVKTPAKF----YILSIVMGFVIAI 116 + L YL I I +LL+ VL + D KTP +++I++ +++ Sbjct: 105 GEVAELAQDYLRILILGIPAYLLNFVLRGFLRGQGDTKTPMYITLIGNVINIILNYILIF 164 Query: 117 GLFPFIGGYGIATAEVSWVWVNTICLAVALLKRRQIDL 154 G F F+G G A A V W+ + L + K ++I L Sbjct: 165 GKFGFLGIVGAALATVISYWLMFLLLLYYIKKAKKIGL 202 >gnl|CDD|180055 PRK05398, PRK05398, formyl-coenzyme A transferase; Provisional. Length = 416 Score = 29.2 bits (66), Expect = 1.1 Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 4/42 (9%) Query: 34 FGIPCTAILLMLPKEII--QTLYERGAFTAQDTILVSSYLSI 73 F IPC +L M KEI +L G D L YL++ Sbjct: 331 FDIPCGPVLSM--KEIAEDPSLRASGTIVEVDHPLRGKYLTV 370 >gnl|CDD|161819 TIGR00326, eubact_ribD, riboflavin biosynthesis protein RibD. This model describes the ribD protein as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region captured in the model dCMP_cyt_deam and shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins believed related to riboflavin biosynthesis contain only this C-terminal domain and are not found as full-length matches to this model. Length = 344 Score = 29.0 bits (65), Expect = 1.1 Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 2/46 (4%) Query: 162 ILSIFISSGLMGMFIVFFKPCLFNQLSAET--AFSPFKNLAIILSG 205 +L F+ GL+ I++ P L A + F+ +A L+ Sbjct: 284 LLGSFLDEGLVDELIIYIAPKLLGGTHAPGLCSEPGFQKMADALNF 329 >gnl|CDD|179519 PRK02983, lysS, lysyl-tRNA synthetase; Provisional. Length = 1094 Score = 28.8 bits (65), Expect = 1.2 Identities = 26/117 (22%), Positives = 45/117 (38%), Gaps = 13/117 (11%) Query: 75 STEIVGFLLSRVLL-------SEFYARNDVKTPAK---FYILSIVMGFVIAIGLFPFIGG 124 S I+GF + V + EF AR K + + +G ++ GL G Sbjct: 111 SLSIIGFAVHVVAIVLLVLARREFPARVRRGALRKALAVLVGGLAVGILVGWGLVELFPG 170 Query: 125 YGIATAEVSWVWVNTICLAVALLKRRQID-LPFQTIYRILSIFISSGLMGMFIVFFK 180 +A E +N + + AL P + +L +F ++ L+ IV F+ Sbjct: 171 -SLAPPERLGWALNRV-VGFALADPDLFTGHPPVWVNALLGLFGAAALIAALIVLFR 225 >gnl|CDD|163065 TIGR02900, spore_V_B, stage V sporulation protein B. SpoVB is the stage V sporulation protein B of the bacterial endopore formation program in Bacillus subtilis and various other Firmcutes. It is nearly universal among endospore-formers. Paralogs with rather high sequence similarity to SpoVB exist, including YkvU in B. subtilis and a number of proteins in the genus Clostridium. Member sequences for the seed alignment were chosen to select those proteins, no more than one to a genome, closest to B. subtilis SpoVB in a neighbor joining tree. Length = 488 Score = 28.4 bits (64), Expect = 1.8 Identities = 48/211 (22%), Positives = 72/211 (34%), Gaps = 25/211 (11%) Query: 3 ALLPKLSSAIQLENKQQSSELRNRAIEYVLFFGIPCTAILLMLPKEIIQTLYERGAFTAQ 62 AL+P +S A+ +N + N+AI+ L G+ T ILL++P E+ Y R A Sbjct: 294 ALVPDISEAMAKKNYSSIEKRINQAIKISLLLGLITTVILLVIPDELGALFYGRPD--AG 351 Query: 63 DTILVSSYLSIYSTEIVGFLLSRVLLSEFYARNDVKTPAKFYILSIVMGFVIAIGLF--- 119 + I V + + S L S K I I I LF Sbjct: 352 NFIRVLAPSFPF------LYFSAPLQSILQGLGKQKVA--LRNSLIGAIVKI-ILLFVLT 402 Query: 120 --PFIGGYGIATAEVSWVWVNTICLAVALLKRRQIDLPFQTIYRILSIFISSGLMGMFIV 177 P I YG A + + TI + K +I + IF G++ + Sbjct: 403 SIPSINIYGYAITFIITSVLVTILNLAEIKKNIRITIDLSDFL----IFALLGILVYLGL 458 Query: 178 FFKPCLFNQLSAETAFSPFKNLAIILSGAVL 208 + L II+ G L Sbjct: 459 SLL-----KYIIFNPNILINLLLIIILGFSL 484 >gnl|CDD|132297 TIGR03253, oxalate_frc, formyl-CoA transferase. This enzyme, formyl-CoA transferase, transfers coenzyme A from formyl-CoA to oxalate. It forms a pathway, together with oxalyl-CoA decarboxylase, for oxalate degradation; decarboxylation by the latter gene regenerates formyl-CoA. The two enzymes typically are encoded by a two-gene operon. Length = 415 Score = 27.5 bits (61), Expect = 3.1 Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 2/50 (4%) Query: 2 AALLPKLSSAIQLENKQQSSELRNRAIEYVLFFGIPCTAILLMLPKEIIQ 51 A PKL+ +++ + E++ +GIPC +L M KEI + Sbjct: 298 EARQPKLNDIFAFIETYTATKDKFEVTEWLNQYGIPCGPVLSM--KEIAE 345 >gnl|CDD|177946 PLN02312, PLN02312, acyl-CoA oxidase. Length = 680 Score = 27.0 bits (60), Expect = 4.3 Identities = 12/34 (35%), Positives = 17/34 (50%) Query: 4 LLPKLSSAIQLENKQQSSELRNRAIEYVLFFGIP 37 L P + ++ E + ELR A+ V FGIP Sbjct: 625 LSPDNVALVRKEVAKLCGELRPHALALVSSFGIP 658 >gnl|CDD|180891 PRK07219, PRK07219, DNA topoisomerase I; Validated. Length = 822 Score = 26.1 bits (58), Expect = 8.0 Identities = 7/18 (38%), Positives = 10/18 (55%) Query: 48 EIIQTLYERGAFTAQDTI 65 +II+ LY+RG D Sbjct: 499 DIIEKLYKRGYVIEGDPP 516 >gnl|CDD|172654 PRK14166, PRK14166, bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional. Length = 282 Score = 26.1 bits (57), Expect = 8.2 Identities = 11/38 (28%), Positives = 22/38 (57%), Gaps = 7/38 (18%) Query: 7 KLSSAIQLENKQQSSELRNRAIEYVLFFGIPCTAILLM 44 LS+ I+ E K+++ L+++ IE C A++L+ Sbjct: 8 ALSAKIKEELKEKNQFLKSKGIE-------SCLAVILV 38 >gnl|CDD|165371 PHA03087, PHA03087, G protein-coupled chemokine receptor-like protein; Provisional. Length = 335 Score = 25.9 bits (57), Expect = 8.3 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 7/84 (8%) Query: 64 TILVSSYLSIYSTEIVGFLLSRVLLSEFYARNDVKTPAKFYILSIVMGFVIAIGLFPFIG 123 TIL+ Y +I+ +VG ++ +L+ + +KTP Y+L++ + ++ + PF Sbjct: 41 TILIVVYSTIFFFGLVGNIIVIYVLT----KTKIKTPMDIYLLNLAVSDLLFVMTLPFQI 96 Query: 124 GYGIATAEVSWVWVNTICLAVALL 147 Y I W + C V+ L Sbjct: 97 YYYILF---QWSFGEFACKIVSGL 117 >gnl|CDD|152433 pfam11998, DUF3493, Protein of unknown function (DUF3493). This family of proteins is functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 79 to 331 amino acids in length. Length = 75 Score = 25.7 bits (57), Expect = 9.6 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 6/55 (10%) Query: 155 PFQTIYRILSI-FISSGLMGMFIVFFKPCLFNQLSAETAFSPFKNLAIILSGAVL 208 PF+ + R L + F +S +G+FI+ F+ ++ NLAI + L Sbjct: 16 PFRGLRRFLYLAFAASAGLGLFIMLFR-----LIAGPDLLETLPNLAIQIGAVAL 65 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.329 0.142 0.411 Gapped Lambda K H 0.267 0.0638 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,720,799 Number of extensions: 239325 Number of successful extensions: 802 Number of sequences better than 10.0: 1 Number of HSP's gapped: 795 Number of HSP's successfully gapped: 70 Length of query: 235 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 145 Effective length of database: 4,049,753 Effective search space: 587214185 Effective search space used: 587214185 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 56 (25.5 bits)