RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780571|ref|YP_003064984.1| hypothetical protein
CLIBASIA_02290 [Candidatus Liberibacter asiaticus str. psy62]
         (182 letters)



>gnl|CDD|149078 pfam07811, TadE, TadE-like protein.  The members of this family
          are similar to a region of the protein product of the
          bacterial tadE locus. In various bacterial species, the
          tad locus is closely linked to flp-like genes, which
          encode proteins required for the production of pili
          involved in adherence to surfaces. It is thought that
          the tad loci encode proteins that act to assemble or
          export an Flp pilus in various bacteria. All tad loci
          but TadA have putative transmembrane regions, and in
          fact the region in question is this family has a high
          proportion of hydrophobic amino acid residues.
          Length = 43

 Score = 39.7 bits (94), Expect = 5e-04
 Identities = 12/42 (28%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 17 GVVAVEMAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMG 58
          G  AVE A++LP+LLL+   + E+      ++++ + A+   
Sbjct: 1  GAAAVEFALVLPVLLLLLFGIVELG-RLFYARQVLQNAAREA 41


>gnl|CDD|183508 PRK12408, PRK12408, glucokinase; Provisional.
          Length = 336

 Score = 30.1 bits (68), Expect = 0.32
 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 9/75 (12%)

Query: 8   ILRFLSRENGVVAVEMAIILPILLLIYMAVYEI---TMLYTLSKRLTRFASHMGDMVAQE 64
           +L+ L R    V +E  +  P LL +Y A+  +   T ++     +T  A    D +A E
Sbjct: 191 LLQHLLRTRTHVPIEHVLSGPGLLNLYRALCALRGATPVHASPAAITAAALAGDDALAHE 250

Query: 65  TSINKQYLQGFENFL 79
                  LQ F  FL
Sbjct: 251 A------LQVFCGFL 259


>gnl|CDD|131469 TIGR02416, CO_dehy_Mo_lg, carbon-monoxide dehydrogenase, large
           subunit.  This model represents the large subunits of
           group of carbon-monoxide dehydrogenases that include
           molybdenum as part of the enzymatic cofactor. There are
           various forms of carbon-monoxide dehydrogenase;
           Salicibacter pomeroyi DSS-3, for example, has two forms.
           Note that, at least in some species, the active site Cys
           is modified with a selenium attached to (rather than
           replacing) the sulfur atom. This is termed
           selanylcysteine, and created post-translationally, in
           contrast to selenocysteine incorporation during
           translation as for many other selenoproteins.
          Length = 770

 Score = 29.9 bits (67), Expect = 0.45
 Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 4/49 (8%)

Query: 44  YTLSKRLTR---FASHMGDMVAQETSINKQYLQGFENFLRATMYPYRTP 89
           Y  S R+T          D +AQ   ++   L+  +NF++   +PY  P
Sbjct: 358 YRCSFRVTEAVYAIERAVDTLAQRLEMDSADLR-IKNFIQPEQFPYTAP 405


>gnl|CDD|183189 PRK11546, zraP, zinc resistance protein; Provisional.
          Length = 143

 Score = 27.1 bits (60), Expect = 2.9
 Identities = 21/90 (23%), Positives = 39/90 (43%), Gaps = 11/90 (12%)

Query: 98  YWLDNKQIVRKMWNWSSSNVKVEREDIPASIKD---ASTFIVRAEVS---INYRTLVFSK 151
           +W         MW  +++ +  E++     I +   A T  +R ++      Y  L+ + 
Sbjct: 29  HWGGGH----GMWQQNAAPLTTEQQAAWQKIHNDFYAQTSALRQQLVSKRYEYNALLTAN 84

Query: 152 ILPDSLKGDIVLRKVYYYRQRLGDQIVCRD 181
             PDS K + V +++   RQ L +  V RD
Sbjct: 85  P-PDSSKINAVAKEMENLRQSLDELRVKRD 113


>gnl|CDD|162834 TIGR02391, hypoth_ymh, conserved hypothetical protein TIGR02391. 
          This family consists of a relatively rare (~ 8
          occurrences per 200 genomes) prokaryotic protein
          family. Genes for members are appear to be associated
          variously with phage and plasmid regions, restriction
          system loci, transposons, and housekeeping genes. The
          function is unknown.
          Length = 125

 Score = 27.0 bits (60), Expect = 3.1
 Identities = 13/61 (21%), Positives = 20/61 (32%), Gaps = 9/61 (14%)

Query: 36 AVYEITMLYTLSKRLTR--FASHMGDMVA-----QETSINKQYLQGFENFLRATMYPYRT 88
           + E+T        L    F+S     V       E    +Q  +G  N L   +  +R 
Sbjct: 32 KIRELTGDSLDGVELIDQAFSSKNNPKVGGNLLQTEAEQGEQ--EGLSNLLAGAITGFRN 89

Query: 89 P 89
          P
Sbjct: 90 P 90


>gnl|CDD|152009 pfam11573, Med23, Mediator complex subunit 23.  Med23 is one of the
           subunits of the Tail portion of the Mediator complex
           that regulates RNA polymerase II activity. Med23 is
           required for heat-shock-specific gene expression, and
           has been shown to mediate transcriptional activation of
           E1A in mice.
          Length = 1341

 Score = 26.7 bits (59), Expect = 3.8
 Identities = 37/198 (18%), Positives = 60/198 (30%), Gaps = 64/198 (32%)

Query: 1   MKCIKNYILRFLSRENGVVAVEMAIILPILLLI----------YMAVYEITMLY------ 44
           MK I    LRF    +  +  ++  +  ++L I          Y  + EI  L+      
Sbjct: 144 MKYILEKALRFPYSVSPEIVPQLLAVEEVILHIFDRNANLLPAYFTLNEIMRLHPYQAAM 203

Query: 45  ---TLSKRLTRFASHMGDMVAQETSINKQYLQGFENFLRATMYPYRTPNHSIIVTGYWLD 101
               L+  L   +      +AQ  SI      G     R++M P     HS     Y   
Sbjct: 204 PPWRLTNLLANLSEEF-RPIAQMLSI-----CG-----RSSMLP--IVEHS----SYA-- 244

Query: 102 NKQIVRKMWNWSSSNVKVEREDIPASIKDASTFIVRAEVSINYRTLVFSKILPDSLKGDI 161
                    NW        + D      +   F ++    + YR  +    L        
Sbjct: 245 -----DNTSNW-------WKLDP-----NTLKFELQGNHKLPYRPELLEPQLY------- 280

Query: 162 VLRKVYYYRQRLGDQIVC 179
           +LR  Y   Q     ++C
Sbjct: 281 LLR--YVLEQPYSRDMLC 296


>gnl|CDD|184750 PRK14568, vanB, D-alanine--D-lactate ligase; Provisional.
          Length = 343

 Score = 26.2 bits (58), Expect = 4.5
 Identities = 10/31 (32%), Positives = 18/31 (58%)

Query: 118 KVEREDIPASIKDASTFIVRAEVSINYRTLV 148
           ++ +E+ P    + ST IV A++S   R+ V
Sbjct: 242 RIHQENEPEKGSENSTIIVPADISAEERSRV 272


>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
           MsbA.  This family consists of a single polypeptide
           chain transporter in the ATP-binding cassette (ABC)
           transporter family, MsbA, which exports lipid A. It may
           also act in multidrug resistance. Lipid A, a part of
           lipopolysaccharide, is found in the outer leaflet of the
           outer membrane of most Gram-negative bacteria. Members
           of this family are restricted to the Proteobacteria
           (although lipid A is more broadly distributed) and often
           are clustered with lipid A biosynthesis genes.
          Length = 571

 Score = 25.4 bits (56), Expect = 9.2
 Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 9/53 (16%)

Query: 23  MAIILPILLLIYMAVYEITMLYTLSKRLTRFASHMGDMVAQETSINKQYLQGF 75
           + ++LP+L ++   V         SKRL R +  + + + Q T++ ++ LQG+
Sbjct: 160 VVVMLPVLSILMRRV---------SKRLRRISKEIQNSMGQVTTVAEETLQGY 203


>gnl|CDD|162277 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
           regulator (CFTR).  The model describes the cystis
           fibrosis transmembrane conductor regulator (CFTR) in
           eukaryotes. The principal role of this protein is
           chloride ion conductance. The protein is predicted to
           consist of 12 transmembrane domains. Mutations or
           lesions in the genetic loci have been linked to the
           aetiology of asthma, bronchiectasis, chronic obstructive
           pulmonary disease etc. Disease-causing mutations have
           been studied by 36Cl efflux assays in vitro cell
           cultures and electrophysiology, all of which point to
           the impairment of chloride channel stability and not the
           biosynthetic processing per se.
          Length = 1490

 Score = 25.3 bits (55), Expect = 9.8
 Identities = 24/108 (22%), Positives = 44/108 (40%), Gaps = 21/108 (19%)

Query: 75  FENFLRATMYPYRTP-----NHSIIVTGYWLDNKQIVRKMWNWSSSNVKVEREDIPASIK 129
           F+  L   M PYR       +  + +T   ++N Q V K + W  +      E I  +I+
Sbjct: 237 FQACLGQKMMPYRDKRAGKISERLAITSEIIENIQSV-KAYCWEEA-----MEKIIKNIR 290

Query: 130 DASTFIVRAEVSINYRT----------LVFSKILPDSLKGDIVLRKVY 167
                + R    + Y            +VF  ++P +L   I+LR+++
Sbjct: 291 QDELKLTRKIAYLRYFYSSAFFFSGFFVVFLSVVPYALIKGIILRRIF 338


  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    0.138    0.411 

Gapped
Lambda     K      H
   0.267   0.0590    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,946,526
Number of extensions: 174247
Number of successful extensions: 426
Number of sequences better than 10.0: 1
Number of HSP's gapped: 426
Number of HSP's successfully gapped: 19
Length of query: 182
Length of database: 5,994,473
Length adjustment: 87
Effective length of query: 95
Effective length of database: 4,114,577
Effective search space: 390884815
Effective search space used: 390884815
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 (21.7 bits)
S2: 54 (24.9 bits)