RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= 537021.9.peg.788_1
         (270 letters)



>gnl|CDD|162764 TIGR02212, lolCE, lipoprotein releasing system, transmembrane
           protein, LolC/E family.  This model describes the LolC
           protein, and its paralog LolE found in some species.
           These proteins are homologous to permease proteins of
           ABC transporters. In some species, two paralogs occur,
           designated LolC and LolE. In others, a single form is
           found and tends to be designated LolC.
          Length = 411

 Score =  233 bits (596), Expect = 4e-62
 Identities = 95/262 (36%), Positives = 145/262 (55%), Gaps = 3/262 (1%)

Query: 6   RFEVIVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGIN 65
              + +A RYL + R+N F+S  S  S IG+ +GV ALIVV+SVMNGF  ++++R+LG+ 
Sbjct: 1   PLSLFIALRYLRAKRRNRFVSFISLFSIIGIALGVAALIVVLSVMNGFERELLQRILGVI 60

Query: 66  GHVVIQQKYYPLVDYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSD 125
            H +I+ K  P++D+Q +  R+   P V    P VSGQA V   +   SGV VRG+  SD
Sbjct: 61  PHAIIESKQNPIIDWQELLERILKNPGVKAAAPIVSGQALVQS-AGKVSGVQVRGVDPSD 119

Query: 126 FSYLQNSFSRFYGNVSNDFDRGK-GVIIGKDLARNLGISIGDKINILSPYGDVTPMGMGI 184
              L    +         F  G+  +IIG+ LA  LG+S+GDKI ++SP  +VTP G   
Sbjct: 120 EDKLSAISNNVKQGALKGFKPGEYNIIIGEQLAEKLGVSVGDKITLISPESNVTPFGEIP 179

Query: 185 RSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTHENI 244
           R K +TV+G+F     + D  +  M L++AQ +    + V+G+ + + DP   +   + +
Sbjct: 180 RQKRFTVIGIFSTGG-EVDGYLALMPLEDAQRFLRYGDQVTGLRLKLDDPFQADALAQQV 238

Query: 245 VRILGNGVVVIDWQQRYQIFFS 266
              LG  + V DW  +    FS
Sbjct: 239 EPELGPELYVRDWTDQNGELFS 260


>gnl|CDD|182995 PRK11146, PRK11146, outer membrane-specific lipoprotein transporter
           subunit LolE; Provisional.
          Length = 412

 Score =  103 bits (258), Expect = 7e-23
 Identities = 67/263 (25%), Positives = 118/263 (44%), Gaps = 25/263 (9%)

Query: 11  VAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVI 70
           +  R+    R+   +S+ S IS IG+ +GV  LIV +S MNGF  ++  R+L +  H  I
Sbjct: 7   IGLRFSRGRRRGGMVSLISVISTIGIALGVAVLIVGLSAMNGFERELNNRILAVVPHGEI 66

Query: 71  QQKYYPLVDYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGS---GVLVRGISNSDFS 127
           +    P  ++Q    R+  +P +    P+V+     +GL   G+    V V+G+      
Sbjct: 67  EAVNQPFTNWQEALARVQKVPGIAAAAPYVN----FTGLVENGAKLKAVQVKGVDPQ--- 119

Query: 128 YLQNSFSRFYGNVSND----FDRGK-GVIIGKDLARNLGISIGDKINILSPYGDVTPMGM 182
             +   S     V ND    F  G+  +I+GK +A  L +  GD + ++ P  +     +
Sbjct: 120 -QEQRVSALPSFVQNDAWQNFKAGEQQIILGKGVADALKVKQGDWVTLMIPNSNPDHKLL 178

Query: 183 GIRSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTHE 242
             +     V G+ ++     D+ +  + L +AQ Y ++ ++V+GI + V D     K   
Sbjct: 179 QPKRVRLQVAGILQLS-GQLDHSLALIPLADAQQYLDMGDSVTGIALKVTDVFNANK--- 234

Query: 243 NIVRILGNG----VVVIDWQQRY 261
            +VR  G      V +  W   Y
Sbjct: 235 -LVRDAGEVTNSYVYIKSWIGTY 256


>gnl|CDD|131268 TIGR02213, lolE_release, lipoprotein releasing system,
           transmembrane protein LolE.  This protein is part of an
           unusual ABC transporter complex that releases
           lipoproteins from the periplasmic side of the bacterial
           inner membrane, rather than transport any substrate
           across the inner membrane. In some species, the
           permease-like transmembrane protein is represented by
           two paralogs, LolC and LolE, both in the LolCDE complex.
           This family consists of LolE, as found in E. coli and
           related species.
          Length = 411

 Score =  100 bits (250), Expect = 4e-22
 Identities = 65/257 (25%), Positives = 118/257 (45%), Gaps = 11/257 (4%)

Query: 10  IVAWRYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVV 69
           ++ WR+    ++N  +S+ S  S IG+ +GV  LIV +S MNGF  ++ +R+L +  H  
Sbjct: 5   LIGWRFSRGKQRNPMVSLISKFSTIGIALGVAVLIVGLSAMNGFERELNQRILAVVPHAE 64

Query: 70  IQQKYYPLVDYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGS---GVLVRGISNSDF 126
           I+    P+ ++Q +  RL   P +    P+VS     +GL   GS    V V+G+     
Sbjct: 65  IESVPPPIHNWQNLEKRLQQNPQIKAAAPYVS----FTGLVENGSKLKAVQVKGV-EPQA 119

Query: 127 SYLQNSFSRFY-GNVSNDFDRGKG-VIIGKDLARNLGISIGDKINILSPYGDVTPMGMGI 184
               +S   F      N F++G+G +I+G  +A+ L + +GD + +L P  +        
Sbjct: 120 EQKVSSIGNFVQEQAWNKFEKGEGQLILGSGVAKELDVKVGDWVTLLIPQQNGDEKFAQP 179

Query: 185 RSKSYTVLGMFRMRFPDYDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTHENI 244
           +     V G+ R+     D+    + L +AQ Y    + V+GI + + D         ++
Sbjct: 180 KRVRVQVTGILRLD-GQLDHSYALLPLADAQQYLTYGDQVTGIALKLDDVFNARNLVRSM 238

Query: 245 VRILGNGVVVIDWQQRY 261
                  V +  W  ++
Sbjct: 239 GNDYPQYVYMQSWISKF 255


>gnl|CDD|182753 PRK10814, PRK10814, outer membrane-specific lipoprotein transporter
           subunit LolC; Provisional.
          Length = 399

 Score = 88.2 bits (219), Expect = 2e-18
 Identities = 72/257 (28%), Positives = 126/257 (49%), Gaps = 16/257 (6%)

Query: 14  RYLFSNRKNAFISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQK 73
           RY+     + F    S++S IG+ +GVMAL+ V+SVMNGF  ++   +LG+    +I  +
Sbjct: 12  RYMRGRAADRFGRFVSWLSTIGITLGVMALVTVLSVMNGFERELQNNILGLMPQAIITSE 71

Query: 74  YYPLVDYQFIANRLDFIPDVIKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSF 133
           +  L   Q  A+ L  +  V ++ P  +G   +    S   GV++ GI  +    L    
Sbjct: 72  HGSLNPQQLPASALK-LDGVNRIAPLTTGDVVLQSARSVAVGVML-GIDPAQKDPL---- 125

Query: 134 SRFYGNVS-NDFDRGK-GVIIGKDLARNLGISIGDKINILSP-YGDVTPMGMGIRSKSYT 190
           + +  NV   D   GK  VI+G+ LA  LG+  GD+I ++ P     TPMG     + +T
Sbjct: 126 TPYLVNVKQTDLQPGKYNVILGEQLAGQLGVKRGDQIRLMVPSASQFTPMGRIPSQRLFT 185

Query: 191 VLGMFRMRFPDYDNGMVYMSLQEAQ--LYFNLENAVSGIEVFVKDPDAIEKTHENIVRIL 248
           V+G F     + D   + ++ Q+A   + +   N ++G  +++ +P  ++   +   + L
Sbjct: 186 VIGTFAAN-SEVDGYQMLVNQQDASRLMRYPAGN-ITGWRLWLDEPLKVDSLSQ---QKL 240

Query: 249 GNGVVVIDWQQRYQIFF 265
             G V  DW++R    F
Sbjct: 241 PEGTVWKDWRERKGELF 257


>gnl|CDD|147920 pfam06021, Gly_acyl_tr_N, Aralkyl acyl-CoA:amino acid
           N-acyltransferase.  This family consists of several
           mammalian specific aralkyl acyl-CoA:amino acid
           N-acyltransferase (glycine N-acyltransferase) proteins
           EC:2.3.1.13.
          Length = 205

 Score = 29.0 bits (65), Expect = 1.4
 Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 10/66 (15%)

Query: 198 RFPDYDNGMVYMSLQEAQLYFNLENAVSGIEVFVKDPDAIEKTHENIVRILGNGVVVIDW 257
           ++PD++   V +  QE ++  +L++  +  +V+ KDP   ++        LG+  V I+W
Sbjct: 48  KWPDFN--TVVIRPQEQEMTDDLDHYTNTYQVYSKDPKKCQE-------FLGSSEV-INW 97

Query: 258 QQRYQI 263
           +Q  QI
Sbjct: 98  KQHLQI 103


>gnl|CDD|163029 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
           synthase PfaA.  Members of the seed for this alignment
           are involved in omega-3 polyunsaturated fatty acid
           biosynthesis, such as the protein PfaA from the
           eicosapentaenoic acid biosynthesis operon in
           Photobacterium profundum strain SS9. PfaA is encoded
           together with PfaB, PfaC, and PfaD, and the functions of
           the individual polypeptides have not yet been described.
           More distant homologs of PfaA, also included with the
           reach of this model, appear to be involved in
           polyketide-like biosynthetic mechanisms of
           polyunsaturated fatty acid biosynthesis, an alternative
           to the more familiar iterated mechanism of chain
           extension and desaturation, and in most cases are
           encoded near genes for homologs of PfaB, PfaC, and/or
           PfaD.
          Length = 2582

 Score = 28.0 bits (62), Expect = 2.3
 Identities = 31/119 (26%), Positives = 50/119 (42%), Gaps = 28/119 (23%)

Query: 40  VMALIVVMSVMN------GFREDMIKRVLGINGHVVIQQKYYPLVDYQFIANRLDFIPDV 93
           +++L+V   V+N      G+  D I   LG+ G    Q++   L        RL + P +
Sbjct: 95  LLSLVVAKEVLNDAGLPDGYDRDKIGITLGVGGG---QKQSSSL------NARLQY-PVL 144

Query: 94  IKVLPFVSGQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNV-----SNDFDRG 147
            KV          SG+    S +L++   +    + +NSF    GNV     +N FD G
Sbjct: 145 KKVFK-------ASGVEDEDSEMLIKKFQDQYIHWEENSFPGSLGNVISGRIANRFDLG 196


>gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily.  This
           subfamily of the AAA family ATPases includes two members
           each from three archaeal species. It also includes yeast
           CDC48 (cell division control protein 48) and the human
           ortholog, transitional endoplasmic reticulum ATPase
           (valosin-containing protein). These proteins in
           eukaryotes are involved in the budding and transfer of
           membrane from the transitional endoplasmic reticulum to
           the Golgi apparatus.
          Length = 733

 Score = 27.9 bits (62), Expect = 2.7
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 3/54 (5%)

Query: 120 GISNSDFSYLQNSFSRFYGNVSNDF--DRGKGVI-IGKDLARNLGISIGDKINI 170
           G+   DF  ++         V      D G+G+I +   L  N G++IGD + +
Sbjct: 30  GVEPGDFVEIEKGDRSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTV 83


>gnl|CDD|162554 TIGR01840, esterase_phb, esterase, PHB depolymerase family.  This
           model describes a subfamily among lipases of the
           ab-hydrolase family. This subfamily includes bacterial
           depolymerases for poly(3-hydroxybutyrate) (PHB) and
           related polyhydroxyalkanoates (PHA), as well as acetyl
           xylan esterases, feruloyl esterases, and others from
           fungi.
          Length = 212

 Score = 27.8 bits (62), Expect = 3.3
 Identities = 9/24 (37%), Positives = 14/24 (58%)

Query: 103 QAFVSGLSSGGSGVLVRGISNSDF 126
           + +V+GLS+GG    V G +  D 
Sbjct: 96  RVYVTGLSAGGGMTAVLGCTYPDV 119


>gnl|CDD|117906 pfam09364, XFP_N, XFP N-terminal domain.  Bacterial enzyme splits
           fructose-6-P and/or xylulose-5-P with the aid of
           inorganic phosphate into either acetyl-P and
           erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P
           EC:4.1.2.9, EC:4.1.2.22. This family is distantly
           related to transketolases e.g. pfam02779.
          Length = 379

 Score = 27.4 bits (61), Expect = 3.9
 Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 7/41 (17%)

Query: 105 FVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDFD 145
           +V G   GG  ++         SYL+ S+S FY  ++ D +
Sbjct: 76  YVVGPGHGGPAMVSP-------SYLEGSYSEFYPEITFDEE 109


>gnl|CDD|181450 PRK08493, PRK08493, NADH dehydrogenase subunit G; Validated.
          Length = 819

 Score = 27.4 bits (61), Expect = 4.4
 Identities = 10/58 (17%), Positives = 25/58 (43%), Gaps = 2/58 (3%)

Query: 123 NSDFSYLQNSFSRF--YGNVSNDFDRGKGVIIGKDLARNLGISIGDKINILSPYGDVT 178
                YL N  ++F  + N + + +   G+ + +   + L +  GD + +     ++T
Sbjct: 720 IGINIYLANPITQFNNFTNKAENLNEKAGLYVSEAFLKKLNLKDGDNVTLKKEEEELT 777


>gnl|CDD|152078 pfam11642, Blo-t-5, Mite allergen Blo t 5.  This family of proteins
           is Blo t 5, an allergen protein from Blomia tropicalis
           mites. This protein shoes strong reactivity with IgE in
           asthmatic and rhinitis patients. The structure of the
           protein contains three alpha helices which form a
           coiled-coil.
          Length = 112

 Score = 27.0 bits (60), Expect = 5.2
 Identities = 8/22 (36%), Positives = 13/22 (59%)

Query: 218 FNLENAVSGIEVFVKDPDAIEK 239
           FN E A++  +V +KD   + K
Sbjct: 83  FNFEAALATGKVLLKDLKELAK 104


>gnl|CDD|183542 PRK12465, PRK12465, xylose isomerase; Provisional.
          Length = 445

 Score = 26.9 bits (59), Expect = 5.2
 Identities = 19/48 (39%), Positives = 22/48 (45%)

Query: 156 LARNLGISIGDKINILSPYGDVTPMGMGIRSKSYTVLGMFRMRFPDYD 203
           LAR+ G SIG K N L     + PM       S TV+G  R    D D
Sbjct: 223 LARDYGRSIGFKGNFLIEPKPMEPMKHQYDFDSATVIGFLRQHGLDQD 270


>gnl|CDD|185385 PRK15488, PRK15488, thiosulfate reductase PhsA; Provisional.
          Length = 759

 Score = 26.6 bits (59), Expect = 6.9
 Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 9/42 (21%)

Query: 150 VIIGKDLARNLGISIGDKINILSPYGD------VTPMGMGIR 185
           V I    A  LGI  GD+I + +  G       VTP   GIR
Sbjct: 668 VWIHPQTAGKLGIKNGDEIRLENSVGKEKGKALVTP---GIR 706


>gnl|CDD|178542 PLN02956, PLN02956, PSII-Q subunit.
          Length = 185

 Score = 26.3 bits (58), Expect = 8.4
 Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 2/35 (5%)

Query: 216 LYFNLENAVSGIEVFVKDPDA--IEKTHENIVRIL 248
           LY +L N+V+ ++   +D D   + + +ENIV  L
Sbjct: 144 LYSDLFNSVTKLDYAARDKDETRVWEYYENIVASL 178


>gnl|CDD|185160 PRK15248, PRK15248, fimbrial outer membrane usher protein StbC;
           Provisional.
          Length = 853

 Score = 26.3 bits (58), Expect = 8.6
 Identities = 9/27 (33%), Positives = 15/27 (55%)

Query: 168 INILSPYGDVTPMGMGIRSKSYTVLGM 194
           I++  P G + PMG  + +   T +GM
Sbjct: 773 ISVKMPDGGIPPMGADVFNGEGTNIGM 799


>gnl|CDD|149560 pfam08547, CIA30, Complex I intermediate-associated protein 30
           (CIA30).  This protein is associated with mitochondrial
           Complex I intermediate-associated protein 30 (CIA30) in
           human and mouse. The family is also present in
           Schizosaccharomyces pombe which does not contain the
           NADH dehydrogenase component of complex I, or many of
           the other essential subunits. This means it is possible
           that this family of protein may not be directly involved
           in oxidative phosphorylation.
          Length = 161

 Score = 26.4 bits (59), Expect = 8.6
 Identities = 7/22 (31%), Positives = 11/22 (50%)

Query: 120 GISNSDFSYLQNSFSRFYGNVS 141
           G+S S      +  + F GN+S
Sbjct: 22  GVSTSSLQLSPDGTAVFSGNLS 43


>gnl|CDD|182528 PRK10535, PRK10535, macrolide transporter ATP-binding /permease
           protein; Provisional.
          Length = 648

 Score = 26.2 bits (58), Expect = 8.9
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 24  FISIASFISFIGVMIGVMALIVVMSVMNGFREDMIKRVLGINGHVVIQQ 72
           F+++ + IS +   IGVM +++V SV    RE  I+  +G     V+QQ
Sbjct: 524 FLTLVAVISLVVGGIGVMNIMLV-SVTERTREIGIRMAVGARASDVLQQ 571


>gnl|CDD|162815 TIGR02349, DnaJ_bact, chaperone protein DnaJ.  This model
           represents bacterial forms of DnaJ, part of the
           DnaK-DnaJ-GrpE chaperone system. The three components
           typically are encoded by consecutive genes. DnaJ
           homologs occur in many genomes, typically not near DnaK
           and GrpE-like genes; most such genes are not included by
           this family. Eukaryotic (mitochondrial and chloroplast)
           forms are not included in the scope of this family.
          Length = 354

 Score = 26.0 bits (58), Expect = 9.7
 Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 102 GQAFVSGLSSGGSGVLVRGISNSDFSYLQNSFSRFYGNVSNDFDRGK--GVIIGKDLARN 159
           G A  +G   GG G    G     F    + F  F+G       R +  G   G+DL  +
Sbjct: 65  GHAGFNG-GGGGGGGGFNGFDIGFFGDFGDIFGDFFGG-GGGSGRRRRSGPRRGEDLRYD 122

Query: 160 LGIS 163
           L ++
Sbjct: 123 LELT 126


  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
   0.326    0.143    0.419 

Gapped
Lambda     K      H
   0.267   0.0760    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,711,929
Number of extensions: 319772
Number of successful extensions: 1002
Number of sequences better than 10.0: 1
Number of HSP's gapped: 994
Number of HSP's successfully gapped: 40
Length of query: 270
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 178
Effective length of database: 4,006,537
Effective search space: 713163586
Effective search space used: 713163586
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 (21.6 bits)
S2: 56 (25.3 bits)