RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780203|ref|YP_003064616.1| hypothetical protein
CLIBASIA_00440 [Candidatus Liberibacter asiaticus str. psy62]
         (82 letters)



>gnl|CDD|176195 cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase. 
           (2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent
           medium chain alcohol dehydrogenase, catalyzes the
           NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and
           meso-butanediol to acetoin. BDH functions as a
           homodimer.  NAD(P)(H)-dependent oxidoreductases are the
           major enzymes in the interconversion of alcohols and
           aldehydes, or ketones.  The medium chain alcohol
           dehydrogenase family (MDR) have a NAD(P)(H)-binding
           domain in a Rossmann fold of a beta-alpha form. The
           N-terminal region typically has an all-beta catalytic
           domain. These proteins typically form dimers (typically
           higher plants, mammals) or tetramers (yeast, bacteria),
           and have 2 tightly bound zinc atoms per subunit.
           Sorbitol and aldose reductase are NAD(+) binding
           proteins of the polyol pathway, which interconverts
           glucose and fructose. Sorbitol dehydrogenase is
           tetrameric and has a single catalytic zinc per subunit.
          Length = 351

 Score = 28.7 bits (65), Expect = 0.33
 Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 2/36 (5%)

Query: 1   MDDRKYRPSKEEVRDAFPELIKALEKGLSTFDVEPL 36
           + ++    S    R+ F E+I  L  G    D EPL
Sbjct: 287 LKEKTLTGSICYTREDFEEVIDLLASGK--IDAEPL 320


>gnl|CDD|145544 pfam02461, AMO, Ammonia monooxygenase.  Ammonia monooxygenase plays
           a key role in the nitrogen cycle and degrades a wide
           range of hydrocarbons and halogenated hydrocarbons.
          Length = 245

 Score = 27.4 bits (61), Expect = 0.90
 Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 3/27 (11%)

Query: 13  VRDAFPELIKALEKG-LSTF--DVEPL 36
           VR   PE I+ +E+G L TF  DV P+
Sbjct: 188 VRTGTPEYIRMVERGTLRTFGKDVVPV 214


>gnl|CDD|111365 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein.  This
           protein is covalently attached to the terminii of
           replicating DNA in vivo.
          Length = 548

 Score = 25.8 bits (57), Expect = 2.8
 Identities = 9/19 (47%), Positives = 12/19 (63%)

Query: 11  EEVRDAFPELIKALEKGLS 29
           EEVR    E I+ LE+ L+
Sbjct: 332 EEVRATVAEAIRLLEEELT 350


>gnl|CDD|145578 pfam02514, CobN-Mg_chel, CobN/Magnesium Chelatase.  This family
           contains a domain common to the cobN protein and to
           magnesium protoporphyrin chelatase. CobN is implicated
           in the conversion of hydrogenobyrinic acid a,c-diamide
           to cobyrinic acid. Magnesium protoporphyrin chelatase is
           involved in chlorophyll biosynthesis.
          Length = 1064

 Score = 25.2 bits (56), Expect = 3.9
 Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 5/34 (14%)

Query: 14  RDAFPELIKALEKG---LSTFDVEPLK-NPVKSH 43
           RDAFP LI+ +++    ++  D EP + N V+ H
Sbjct: 787 RDAFPNLIELIDEAVRLVAALD-EPDEMNYVRKH 819


>gnl|CDD|176479 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions primarily to
           fill DNA gaps that arise during DNA repair,
           recombination and replication.  Family A polymerase
           (polymerase I) functions primarily to fill DNA gaps that
           arise during DNA repair, recombination and replication.
           DNA-dependent DNA polymerases can be classified in six
           main groups based upon phylogenetic relationships with
           E. coli polymerase I (classA), E. coli polymerase II
           (class B), E.coli polymerase III (class C),
           euryarchaaeota polymerase II (class D), human polymerase
            beta (class x), E. coli UmuC/DinB and eukaryotic RAP
           30/Xeroderma pigmentosum variant (class Y). Family A
           polymerase are found primarily in organisms related to
           prokaryotes and include prokaryotic DNA polymerase I
           ,mitochondrial polymerase delta, and several
           bacteriphage polymerases including those from
           odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
           have two functional domains located on the same
           polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
           Pol I uses its 5' nuclease activity to remove the
           ribonucleotide portion of newly synthesized Okazaki
           fragments and DNA polymerase activity to fill in the
           resulting gap. A combination of phylogenomic and
           signature sequence-based (or phonetic) approaches is
           used to understand the evolutionary relationships among
           bacteria. DNA polymerase I is one of the conserved
           proteins that is used to search for protein signatures.
           The structure of these polymerases resembles in overall
           morphology a cupped human right hand, with fingers
           (which bind an incoming nucleotide and interact with the
           single-stranded template), palm (which harbors the
           catalytic amino acid residues and also binds an incoming
           dNTP) and thumb (which binds double-stranded DNA)
           subdomains.
          Length = 378

 Score = 24.9 bits (55), Expect = 5.1
 Identities = 8/22 (36%), Positives = 14/22 (63%)

Query: 50  YISHVCELIELLKNKDFDGVEI 71
           Y+  +    EL+K+ DFD +E+
Sbjct: 126 YLKDLDLARELVKSGDFDALEL 147


>gnl|CDD|146970 pfam04587, ADP_PFK_GK, ADP-specific Phosphofructokinase/Glucokinase
           conserved region.  In archaea a novel type of glycolytic
           pathway exists that is deviant from the classical
           Embden-Meyerhof pathway. This pathway utilizes two novel
           proteins: an ADP-dependent Glucokinase and an
           ADP-dependent Phosphofructokinase. This conserved region
           is present at the C-terminal of both these proteins.
           Interestingly this family contains sequences from higher
           eukaryotes..
          Length = 444

 Score = 24.7 bits (54), Expect = 5.3
 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 10/57 (17%)

Query: 10  KEEVRDAFPELIKALE----KGLSTFDVEPLKNPVKSHGKGYESYISHVCELIELLK 62
           KEE+R+   E+ + ++     GL    +        S GK  E Y+  V E I+LLK
Sbjct: 196 KEELREFLEEIGEQVDLAILSGLQMLTLF------YSDGKDAEYYLKRVKEDIKLLK 246


>gnl|CDD|37414 KOG2203, KOG2203, KOG2203, GTP-binding protein [General function
           prediction only].
          Length = 772

 Score = 24.6 bits (53), Expect = 5.6
 Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 6/64 (9%)

Query: 8   PSKEEVRDAFPELIKALEKGLSTFDVEPLKNPVKSHGK----GYESYISHVCELIELLKN 63
             KE   D F E + +L +      + P       HG     G+  Y   + ++IE  +N
Sbjct: 218 SHKELKEDQFKEQVASLRQRFVHSGISPYGFAGDYHGVIPADGFSFYAEQIWDVIE--EN 275

Query: 64  KDFD 67
           KD D
Sbjct: 276 KDLD 279


>gnl|CDD|119349 cd00598, GH18_chitinase-like, The GH18 (glycosyl hydrolase, family
           18) type II chitinases hydrolyze chitin, an abundant
           polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc)
           which is a major component of the cell wall of fungi and
           the exoskeleton of arthropods.  Chitinases have been
           identified in viruses, bacteria, fungi, protozoan
           parasites, insects, and plants. The structure of the
           GH18 domain is an eight-stranded beta/alpha barrel with
           a pronounced active-site cleft at the C-terminal end of
           the beta-barrel.  The GH18 family includes
           chitotriosidase, chitobiase, hevamine, zymocin-alpha,
           narbonin, SI-CLP (stabilin-1 interacting chitinase-like
           protein), IDGF (imaginal disc growth factor), CFLE
           (cortical fragment-lytic enzyme) spore hydrolase, the
           type III and type V plant chitinases, the
           endo-beta-N-acetylglucosaminidases, and the
           chitolectins.  The GH85 (glycosyl hydrolase, family 85)
           ENGases (endo-beta-N-acetylglucosaminidases) are closely
           related to the GH18 chitinases and are included in this
           alignment model..
          Length = 210

 Score = 24.6 bits (54), Expect = 6.6
 Identities = 8/15 (53%), Positives = 10/15 (66%)

Query: 57  LIELLKNKDFDGVEI 71
           L+  LK   FDGV+I
Sbjct: 96  LVSFLKTYGFDGVDI 110


>gnl|CDD|145454 pfam02309, AUX_IAA, AUX/IAA family.  Transcription of the AUX/IAA
           family of genes is rapidly induced by the plant hormone
           auxin. Some members of this family are longer and
           contain an N terminal DNA binding domain. The function
           of this region is uncertain.
          Length = 192

 Score = 24.2 bits (53), Expect = 8.4
 Identities = 11/31 (35%), Positives = 14/31 (45%)

Query: 17  FPELIKALEKGLSTFDVEPLKNPVKSHGKGY 47
           + EL  ALEK  S F +   K     +G  Y
Sbjct: 118 YDELSSALEKMFSCFTIGESKLLDLLNGSEY 148


>gnl|CDD|48477 cd00713, GltS, Glutamine amidotransferases class-II (Gn-AT),
           glutamate synthase (GltS)-type. GltS is a homodimer that
           synthesizes L-glutamate from 2-oxoglutarate and
           L-glutamine, an important step in ammonia assimilation
           in bacteria, cyanobacteria and plants. The N-terminal
           glutaminase domain catalyzes the hydrolysis of glutamine
           to glutamic acid and ammonia, and has a fold similar to
           that of other glutamine amidotransferases such as
           glucosamine-fructose 6-phosphate synthase (GLMS or
           GFAT), glutamine phosphoribosylpyrophosphate (Prpp)
           amidotransferase (GPATase), asparagine synthetase B
           (AsnB), and beta lactam synthetase (beta-LS), as well as
           the Ntn hydrolase folds of the proteasomal alpha and
           beta subunits..
          Length = 413

 Score = 24.0 bits (52), Expect = 9.9
 Identities = 9/21 (42%), Positives = 10/21 (47%)

Query: 60  LLKNKDFDGVEIERKSYNLRK 80
           +      DG   ERK Y LRK
Sbjct: 133 VGAPSGDDGEAFERKLYLLRK 153


  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
   0.313    0.135    0.381 

Gapped
Lambda     K      H
   0.267   0.0660    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,003,449
Number of extensions: 43974
Number of successful extensions: 163
Number of sequences better than 10.0: 1
Number of HSP's gapped: 163
Number of HSP's successfully gapped: 21
Length of query: 82
Length of database: 6,263,737
Length adjustment: 52
Effective length of query: 30
Effective length of database: 5,140,069
Effective search space: 154202070
Effective search space used: 154202070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 51 (23.6 bits)