RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780961|ref|YP_003065374.1| hypothetical protein
CLIBASIA_04310 [Candidatus Liberibacter asiaticus str. psy62]
         (200 letters)



>gnl|CDD|32922 COG3108, COG3108, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 185

 Score =  155 bits (394), Expect = 6e-39
 Identities = 69/149 (46%), Positives = 95/149 (63%), Gaps = 2/149 (1%)

Query: 54  EEVRTLKIYVVSTGSKAIVTFKRGSQYNQEGLSQLNRLLYDWHSKQSIDMDPQLFDFLWE 113
            E R LK+Y + TG KA   FK    Y+Q  LS LNRLL DW   + + MDP+LFD +++
Sbjct: 35  PEPRILKLYNLHTGEKAEAEFKDNGGYDQASLSGLNRLLRDWRQNEVVRMDPRLFDLVYQ 94

Query: 114 IQQYFSVPEYIYILSGYRTQETNKMLSRRNRKIARKSQHVLGKAVDFYIPGVSLRSLYKI 173
           ++        + + SGYR+  TN+ML  R+R +A+KS H+LG+A+DF IPGVSL  L   
Sbjct: 95  LKTLEGHRRPVQVTSGYRSPATNRMLRSRSRGVAKKSLHMLGQAMDFQIPGVSLWELRNA 154

Query: 174 AIRLKRGGVGYY--SKFLHIDVGRVRSWT 200
           A+ ++ GGVGYY  S  +H+DVG VR W 
Sbjct: 155 ALSMQGGGVGYYPHSNSVHMDVGPVRDWN 183


>gnl|CDD|145604 pfam02557, VanY, D-alanyl-D-alanine carboxypeptidase. 
          Length = 131

 Score = 28.8 bits (65), Expect = 0.99
 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 12/54 (22%)

Query: 123 YIYILSGYRTQETNKML---SRRNRKI--ARK-------SQHVLGKAVDFYIPG 164
            ++I SGYR+ E  + L     +      A +       S+H  G A+D   P 
Sbjct: 25  DLFIASGYRSYEYQQALYDKYVKGEGKEAALRYSAPPGYSEHQTGLAIDIGDPD 78


>gnl|CDD|37703 KOG2492, KOG2492, KOG2492, CDK5 activator-binding protein [Signal
           transduction mechanisms].
          Length = 552

 Score = 27.3 bits (60), Expect = 2.9
 Identities = 10/33 (30%), Positives = 16/33 (48%)

Query: 137 KMLSRRNRKIARKSQHVLGKAVDFYIPGVSLRS 169
           ++L    R  +R++   L   +   IPGV L S
Sbjct: 366 RVLEIMRRGYSREAYLELVAHIRSMIPGVGLSS 398


>gnl|CDD|36001 KOG0782, KOG0782, KOG0782, Predicted diacylglycerol kinase [Signal
           transduction mechanisms].
          Length = 1004

 Score = 27.4 bits (60), Expect = 2.9
 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 33  LSPDLIKYHQQSSMSSDLLDQ-EEVRTLKIYVVSTGSKAIVTF 74
           LS DL+K  +       LL Q  +  +L  Y   TG+  IV +
Sbjct: 875 LSSDLMKLQETHLNGGSLLIQGPDHCSLLHYAAKTGNGEIVKY 917


>gnl|CDD|37762 KOG2551, KOG2551, KOG2551, Phospholipase/carboxyhydrolase [Amino
           acid transport and metabolism].
          Length = 230

 Score = 27.2 bits (60), Expect = 3.0
 Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 3/61 (4%)

Query: 115 QQYFSVP--EYIYILSGYRTQETNKMLSRRNRKIARKSQHVLGKAVDFYIPGVSLRSLYK 172
             Y   P  ++   +SG++        S   R ++  S H+ G+  D  +P      L +
Sbjct: 129 LPYVKQPPFKFAVFISGFKFPSKKLDESAYKRPLSTPSLHIFGET-DTIVPSERSEQLAE 187

Query: 173 I 173
            
Sbjct: 188 S 188


>gnl|CDD|37702 KOG2491, KOG2491, KOG2491, Nuclear matrix protein [Nuclear
           structure].
          Length = 674

 Score = 27.3 bits (60), Expect = 3.2
 Identities = 14/66 (21%), Positives = 25/66 (37%), Gaps = 14/66 (21%)

Query: 100 SIDMDPQLFDFLWEIQQYFSVPEYIY--------------ILSGYRTQETNKMLSRRNRK 145
           SI +D  L+   W +Q YFS P  +Y              +L  +++ +        N K
Sbjct: 222 SIKVDYNLYRKFWSLQDYFSNPNSLYEKIKWKKFLKYLEEVLQVFKSYKLEDTFGESNEK 281

Query: 146 IARKSQ 151
           +   + 
Sbjct: 282 MEELAT 287


>gnl|CDD|48525 cd02976, NrdH, NrdH-redoxin (NrdH) family; NrdH is a small
           monomeric protein with a conserved redox active CXXC
           motif within a TRX fold, characterized by a glutaredoxin
           (GRX)-like sequence and TRX-like activity profile. In
           vitro, it displays protein disulfide reductase activity
           that is dependent on TRX reductase, not glutathione
           (GSH). It is part of the NrdHIEF operon, where NrdEF
           codes for class Ib ribonucleotide reductase (RNR-Ib), an
           efficient enzyme at low oxygen levels. Under these
           conditions when GSH is mostly conjugated to spermidine,
           NrdH can still function and act as a hydrogen donor for
           RNR-Ib. It has been suggested that the NrdHEF system may
           be the oldest RNR reducing system, capable of
           functioning in a microaerophilic environment, where GSH
           was not yet available. NrdH from Corynebacterium
           ammoniagenes can form domain-swapped dimers, although it
           is unknown if this happens in vivo. Domain-swapped
           dimerization, which results in the blocking of the TRX
           reductase binding site, could be a mechanism for
           regulating the oxidation state of the protein..
          Length = 73

 Score = 26.3 bits (58), Expect = 6.1
 Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 3/42 (7%)

Query: 101 IDMDPQLFDFLWEIQQYFSVPEYIY---ILSGYRTQETNKML 139
           +D DP+  + L ++  Y SVP  +     LSG+R  +   +L
Sbjct: 32  VDEDPEALEELKKLNGYRSVPVVVIGDEHLSGFRPDKLRALL 73


>gnl|CDD|147498 pfam05343, Peptidase_M42, M42 glutamyl aminopeptidase.  These
           peptidases are found in Archaea and Bacteria. The
           example in Lactococcus lactis, PepA, aids growth on
           milk. Pyrococcus horikoshii contain a thermostable
           de-blocking aminopeptidase member of this family used
           commercially for N-terminal protein sequencing.
          Length = 292

 Score = 26.0 bits (58), Expect = 7.1
 Identities = 8/30 (26%), Positives = 15/30 (50%)

Query: 103 MDPQLFDFLWEIQQYFSVPEYIYILSGYRT 132
             P+L  FL E+ +  ++P  + +  G  T
Sbjct: 221 YHPKLRKFLLELAKKNNIPYQVEVYPGGGT 250


>gnl|CDD|133086 cd06228, Peptidase_M14-like_3, A functionally uncharacterized
           subgroup of the M14 family of metallocarboxypeptidases
           (MCPs). The M14 family are zinc-binding
           carboxypeptidases (CPs) which hydrolyze single,
           C-terminal amino acids from polypeptide chains, and have
           a recognition site for the free C-terminal carboxyl
           group, which is a key determinant of specificity. Two
           major subfamilies of the M14 family, defined based on
           sequence and structural homology, are the A/B and N/E
           subfamilies. Enzymes belonging to the A/B subfamily are
           normally synthesized as inactive precursors containing
           preceding signal peptide, followed by an N-terminal
           pro-region linked to the enzyme; these proenzymes are
           called procarboxypeptidases. The A/B enzymes can be
           further divided based on their substrate specificity;
           Carboxypeptidase A-like (CPA-like) enzymes favor
           hydrophobic residues while carboxypeptidase B-like
           (CPB-like) enzymes only cleave the basic residues lysine
           or arginine. The A forms have slightly different
           specificities, with Carboxypeptidase A1 (CPA1)
           preferring aliphatic and small aromatic residues, and
           CPA2 preferring the bulky aromatic side chains. Enzymes
           belonging to the N/E subfamily enzymes are not produced
           as inactive precursors and instead rely on their
           substrate specificity and subcellular
           compartmentalization to prevent inappropriate cleavages.
           They contain an extra C-terminal transthyretin-like
           domain, thought to be involved in folding or formation
           of oligomers.  MCPs can also be classified based on
           their involvement in specific physiological processes;
           the pancreatic MCPs participate only in alimentary
           digestion and include carboxypeptidase A and B (A/B
           subfamily), while others, namely regulatory MCPs or the
           N/E subfamily, are involved in more selective reactions,
           mainly in non-digestive tissues and fluids, acting on
           blood coagulation/fibrinolysis, inflammation and local
           anaphylaxis, pro-hormone and neuropeptide processing,
           cellular response and others.   Another MCP subfamily,
           is that of succinylglutamate desuccinylase
           /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
           (NAA), and deficiency in which is the established cause
           of Canavan disease. Another subfamily (referred to as
           subfamily C) includes an exceptional type of activity in
           the MCP family, that of dipeptidyl-peptidase activity of
           gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
           which is involved in bacterial cell wall metabolism.
          Length = 332

 Score = 25.9 bits (57), Expect = 8.0
 Identities = 8/12 (66%), Positives = 10/12 (83%)

Query: 108 FDFLWEIQQYFS 119
           FDFLW+ Q+YF 
Sbjct: 130 FDFLWDFQKYFD 141


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.323    0.137    0.403 

Gapped
Lambda     K      H
   0.267   0.0798    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,432,974
Number of extensions: 121372
Number of successful extensions: 328
Number of sequences better than 10.0: 1
Number of HSP's gapped: 326
Number of HSP's successfully gapped: 18
Length of query: 200
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 111
Effective length of database: 4,340,536
Effective search space: 481799496
Effective search space used: 481799496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.8 bits)