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)