RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780412|ref|YP_003064825.1| hypothetical protein
CLIBASIA_01485 [Candidatus Liberibacter asiaticus str. psy62]
         (94 letters)



>gnl|CDD|114945 pfam06253, MTTB, Trimethylamine methyltransferase (MTTB).  This
          family consists of several trimethylamine
          methyltransferase (MTTB) (EC:2.1.1.-) proteins from
          numerous Rhizobium and Methanosarcina species.
          Length = 505

 Score = 29.3 bits (66), Expect = 0.20
 Identities = 9/56 (16%), Positives = 20/56 (35%), Gaps = 7/56 (12%)

Query: 12 ASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEI 67
          A R A          S         ++   +    ++  E++E + R +  + EE+
Sbjct: 7  AGRRAMRGGPGAPQPS-------FPRLVNPIPPYQLLSDEQLERIHRASLRILEEV 55


>gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB.  Members
           of this protein family are the bacterial ATP-dependent
           chaperone ClpB. This protein belongs to the AAA family,
           ATPases associated with various cellular activities
           (pfam00004). This molecular chaperone does not act as a
           protease, but rather serves to disaggregate misfolded
           and aggregated proteins.
          Length = 852

 Score = 28.4 bits (64), Expect = 0.44
 Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 14/63 (22%)

Query: 31  ESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGK--------RLEKIEQQLA 82
           E+ A+I+++  ++S      EE++ + R    L  E  A+ K        RLE +E++LA
Sbjct: 391 EAAARIRME--IDSK----PEELDELDRRIIQLEIEREALKKEKDEASKERLEDLEKELA 444

Query: 83  DLE 85
           +LE
Sbjct: 445 ELE 447


>gnl|CDD|182605 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
           Provisional.
          Length = 638

 Score = 28.2 bits (63), Expect = 0.49
 Identities = 12/26 (46%), Positives = 16/26 (61%)

Query: 60  TSHLREEITAIGKRLEKIEQQLADLE 85
           T  LR+EI  + K +EK+  QLA  E
Sbjct: 558 TQPLRKEIARLEKEMEKLNAQLAQAE 583


>gnl|CDD|162062 TIGR00839, aspA, aspartate ammonia-lyase.  Fumarate hydratase
           scores as high as 570 bits against this model.
          Length = 468

 Score = 27.9 bits (62), Expect = 0.60
 Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 25/87 (28%)

Query: 21  DAFKDISKEAESFAQIKIQRT-------------LNSMGVVRAEEIENVKRTTSHLRE-- 65
           D F+  +KE      +K+ RT               +  ++  EE++N+KRT   L E  
Sbjct: 167 DGFEQKAKEFADI--LKMGRTQLQDAVPMTLGQEFEAFSILLEEEVKNIKRTAELLLEVN 224

Query: 66  -EITAIGKRL-------EKIEQQLADL 84
              TAIG  L         + ++LA++
Sbjct: 225 LGATAIGTGLNTPPEYSPLVVKKLAEV 251


>gnl|CDD|177553 PHA03185, PHA03185, UL14 tegument protein; Provisional.
          Length = 214

 Score = 27.3 bits (60), Expect = 0.94
 Identities = 20/68 (29%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 19  ASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEE-IENVKRTTSHLREEITAIGKRLEKI 77
           A  A +++    +S A++++ R   +   +R EE  E      +H R    A+G+RL++ 
Sbjct: 50  AKAAHRELEARLKSRARLEMLRQHAACVKIRVEEQAERRDFLIAHRRYLDPALGERLDEA 109

Query: 78  EQQLADLE 85
           E +LAD E
Sbjct: 110 EDRLADQE 117


>gnl|CDD|180249 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
          Length = 646

 Score = 26.4 bits (59), Expect = 1.5
 Identities = 15/87 (17%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 5   SNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIEN-VKRTTSHL 63
           SN+  ++   L +  S+A   +         ++ ++    + V   EE+   V+     +
Sbjct: 41  SNERLRKLRSLLTKLSEALDKLRSYLPKLNPLREEK--KKVSVKSLEELIKDVEEELEKI 98

Query: 64  REEITAIGKRLEKIEQQLADLELFINQ 90
            +EI  + + + ++E ++ +LE  I +
Sbjct: 99  EKEIKELEEEISELENEIKELEQEIER 125


>gnl|CDD|163162 TIGR03156, GTP_HflX, GTP-binding protein HflX.  This protein family
           is one of a number of homologous small, well-conserved
           GTP-binding proteins with pleiotropic effects. Bacterial
           members are designated HflX, following the naming
           convention in Escherichia coli where HflX is encoded
           immediately downstream of the RNA chaperone Hfq, and
           immediately upstream of HflKC, a membrane-associated
           protease pair with an important housekeeping function.
           Over large numbers of other bacterial genomes, the
           pairing with hfq is more significant than with hflK and
           hlfC. The gene from Homo sapiens in this family has been
           named PGPL (pseudoautosomal GTP-binding protein-like).
          Length = 351

 Score = 26.7 bits (60), Expect = 1.5
 Identities = 9/19 (47%), Positives = 13/19 (68%)

Query: 62  HLREEITAIGKRLEKIEQQ 80
            +RE I  + K LEK+E+Q
Sbjct: 158 LIRERIAQLKKELEKVEKQ 176


>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
          Length = 426

 Score = 26.2 bits (58), Expect = 1.8
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 63  LREEITAIGKRLEKIEQQ 80
           LR  I  I  RLE++E+Q
Sbjct: 167 LRNRIVQILSRLERVEKQ 184


>gnl|CDD|148090 pfam06273, eIF-4B, Plant specific eukaryotic initiation factor 4B. 
           This family consists of several plant specific
           eukaryotic initiation factor 4B proteins.
          Length = 430

 Score = 26.1 bits (57), Expect = 1.8
 Identities = 21/61 (34%), Positives = 26/61 (42%), Gaps = 8/61 (13%)

Query: 37  KIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIE---QQLADLELFINQKEK 93
           KI   L    V R E  E       +L+EEI  + K L+K E    +       I QKEK
Sbjct: 294 KIDLELEHRRVDRPETEEE-----KNLKEEIELLKKELQKEEARXPKSKGSSELIRQKEK 348

Query: 94  E 94
           E
Sbjct: 349 E 349


>gnl|CDD|183393 PRK12273, aspA, aspartate ammonia-lyase; Provisional.
          Length = 472

 Score = 26.2 bits (59), Expect = 1.9
 Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 29/89 (32%)

Query: 21  DAFKDISKEAESFAQI-KIQRT-------------LNSMGVVRAEEIENVKRTTSHLREE 66
           +AF+  +KE   FA I K+ RT               +  V  AE+ + + R    LR E
Sbjct: 171 EAFEAKAKE---FADILKMGRTQLQDAVPMTLGQEFGAYAVALAEDRKRLYRAAELLR-E 226

Query: 67  I----TAIGKRL-------EKIEQQLADL 84
           +    TAIG  L       E + ++LA++
Sbjct: 227 VNLGATAIGTGLNAPPGYIELVVEKLAEI 255


>gnl|CDD|163395 TIGR03683, A-tRNA_syn_arch, alanyl-tRNA synthetase.  This family of
           alanyl-tRNA synthetases is limited to the archaea, and
           is a subset of those sequences identified by the model
           pfam07973 covering the second additional domain (SAD) of
           alanyl and threonyl tRNA synthetases.
          Length = 902

 Score = 26.1 bits (58), Expect = 2.0
 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 8/81 (9%)

Query: 14  RLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKR 73
           R+   A +A  +  +E E      ++ + + + V   +  E VKR      EE     K 
Sbjct: 729 RIEFAAGEAALEYIQELED----LLRESSDILKVPPEQLPETVKR----FFEEWKEQRKE 780

Query: 74  LEKIEQQLADLELFINQKEKE 94
           +E+++++LA+L+++    E E
Sbjct: 781 IERLKKKLAELKIYELISEAE 801


>gnl|CDD|179074 PRK00591, prfA, peptide chain release factor 1; Validated.
          Length = 359

 Score = 25.8 bits (58), Expect = 2.6
 Identities = 9/30 (30%), Positives = 20/30 (66%)

Query: 63 LREEITAIGKRLEKIEQQLADLELFINQKE 92
          + +++ A+ +R E++E  L+D E+  +QK 
Sbjct: 4  MLDKLEALEERYEELEALLSDPEVISDQKR 33


>gnl|CDD|178488 PLN02900, PLN02900, alanyl-tRNA synthetase.
          Length = 936

 Score = 25.7 bits (57), Expect = 2.7
 Identities = 14/40 (35%), Positives = 19/40 (47%)

Query: 45  MGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADL 84
            G V  E  +N KR T  + EE  + GK LEK  ++    
Sbjct: 360 SGDVFPEVKKNEKRITEIIAEEELSFGKTLEKGIEKFKKA 399


>gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
          Length = 637

 Score = 25.7 bits (57), Expect = 2.8
 Identities = 26/70 (37%), Positives = 35/70 (50%), Gaps = 10/70 (14%)

Query: 21  DAFKDISKEAESFAQIKIQRTL---NSMGVVR-AEEI---ENVKRTTSHLREEITAIGKR 73
           DA ++I +EA+  A  K   TL   +  G+VR A +I   E  + TT    E +    K 
Sbjct: 343 DAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTT---AEHVLEAKKI 399

Query: 74  LEKIEQQLAD 83
              IEQQLAD
Sbjct: 400 ARSIEQQLAD 409


>gnl|CDD|183309 PRK11778, PRK11778, putative inner membrane peptidase; Provisional.
          Length = 330

 Score = 25.6 bits (57), Expect = 2.9
 Identities = 8/11 (72%), Positives = 8/11 (72%)

Query: 60  TSHLREEITAI 70
              LREEITAI
Sbjct: 106 VESLREEITAI 116


>gnl|CDD|182611 PRK10642, PRK10642, proline/glycine betaine transporter;
           Provisional.
          Length = 490

 Score = 25.1 bits (55), Expect = 4.1
 Identities = 7/23 (30%), Positives = 16/23 (69%)

Query: 63  LREEITAIGKRLEKIEQQLADLE 85
           L E    I ++++ I+Q++A+L+
Sbjct: 454 LVEHYDNIEQKIDDIDQEIAELQ 476


>gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
           primarily archaeal type.  SMC (structural maintenance of
           chromosomes) proteins bind DNA and act in organizing and
           segregating chromosomes for partition. SMC proteins are
           found in bacteria, archaea, and eukaryotes. It is found
           in a single copy and is homodimeric in prokaryotes, but
           six paralogs (excluded from this family) are found in
           eukarotes, where SMC proteins are heterodimeric. This
           family represents the SMC protein of archaea and a few
           bacteria (Aquifex, Synechocystis, etc); the SMC of other
           bacteria is described by TIGR02168. The N- and
           C-terminal domains of this protein are well conserved,
           but the central hinge region is skewed in composition
           and highly divergent.
          Length = 1164

 Score = 25.0 bits (55), Expect = 4.2
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 9/84 (10%)

Query: 11  QASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAI 70
           + S+  S AS    +I KE E   Q   +  L        E +E ++   S L +EI  +
Sbjct: 706 ELSQELSDASRKIGEIEKEIEQLEQE--EEKLK-------ERLEELEEDLSSLEQEIENV 756

Query: 71  GKRLEKIEQQLADLELFINQKEKE 94
              L+++E ++ +LE  +++ E+ 
Sbjct: 757 KSELKELEARIEELEEDLHKLEEA 780



 Score = 25.0 bits (55), Expect = 4.4
 Identities = 11/72 (15%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 23  FKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLA 82
           ++ + KE   +   ++ +   ++      + E ++R  + L EE+  + + + ++E++L 
Sbjct: 213 YQALLKEKREYEGYELLKEKEAL----ERQKEAIERQLASLEEELEKLTEEISELEKRLE 268

Query: 83  DLELFINQKEKE 94
           ++E  + +  K+
Sbjct: 269 EIEQLLEELNKK 280



 Score = 23.9 bits (52), Expect = 9.3
 Identities = 10/44 (22%), Positives = 23/44 (52%)

Query: 51  EEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQKEKE 94
           E+  ++K     + +EI  +  + E++E++L +LE  +   E  
Sbjct: 840 EQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAALRDLESR 883


>gnl|CDD|184382 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
          Length = 900

 Score = 24.8 bits (55), Expect = 4.5
 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 4/58 (6%)

Query: 37  KIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQKEKE 94
            ++     +GV   +  + V+R      EE     K +EK+ ++LA+L       + E
Sbjct: 744 LLKEAAEILGVPPEQLPKTVER----FFEEWKEQKKEIEKLRKELAELLASELLSKAE 797


>gnl|CDD|149519 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal.  This
           domain is found to the N-terminus of bacterial signal
           peptidases of the S49 family (pfam01343).
          Length = 154

 Score = 24.8 bits (55), Expect = 5.3
 Identities = 8/11 (72%), Positives = 8/11 (72%)

Query: 60  TSHLREEITAI 70
              LREEITAI
Sbjct: 113 VESLREEITAI 123


>gnl|CDD|161830 TIGR00344, alaS, alanine--tRNA ligase.  The model describes
          alanine--tRNA ligase. This enzyme catalyzes the
          reaction (tRNAala + L-alanine + ATP = L-alanyl-tRNAala
          + pyrophosphate + AMP).
          Length = 851

 Score = 24.7 bits (54), Expect = 6.4
 Identities = 10/24 (41%), Positives = 14/24 (58%)

Query: 40 RTLNSMGVVRAEEIENVKRTTSHL 63
          R +N+   +R  +IENV RT  H 
Sbjct: 55 RLVNAQPCIRLNDIENVGRTARHH 78


>gnl|CDD|180144 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
          Length = 679

 Score = 24.0 bits (53), Expect = 8.1
 Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 4/23 (17%)

Query: 67  ITAIGKRLEKIEQQLADLELFIN 89
           + AI +RLE+ EQ L    LF+N
Sbjct: 356 LEAIKQRLERGEQVL----LFLN 374


>gnl|CDD|150352 pfam09660, DUF2397, Protein of unknown function (DUF2397).
           Proteins in this entry are encoded within a conserved
           gene four-gene neighbourhood found sporadically in a
           phylogenetically broad range of bacteria including:
           Nocardia farcinica, Symbiobacterium thermophilum, and
           Streptomyces avermitilis (Actinobacteria), Geobacillus
           kaustophilus (Firmicutes), Azoarcus sp. EbN1 and
           Ralstonia solanacearum (Betaproteobacteria).
          Length = 478

 Score = 24.2 bits (53), Expect = 8.3
 Identities = 9/28 (32%), Positives = 13/28 (46%)

Query: 58  RTTSHLREEITAIGKRLEKIEQQLADLE 85
               +LR+ I  + +R  KI   L  LE
Sbjct: 187 LLIDYLRDFIRDLQRRSAKIAAALRALE 214


>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
          Length = 880

 Score = 23.9 bits (52), Expect = 9.0
 Identities = 14/43 (32%), Positives = 22/43 (51%)

Query: 51  EEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQKEK 93
           E++E   +    L+EEI  + K LE +E     LE  I + E+
Sbjct: 224 EKLEKEVKELEELKEEIEELEKELESLEGSKRKLEEKIRELEE 266


>gnl|CDD|131666 TIGR02617, tnaA_trp_ase, tryptophanase, leader
          peptide-associated.  Members of this family belong to
          the beta-eliminating lyase family (pfam01212) and act
          as tryptophanase (L-tryptophan indole-lyase). The
          tryptophanases of this family, as a rule, are found
          with a tryptophanase leader peptide (TnaC) encoded
          upstream. Both tryptophanases (4.1.99.1) and tyrosine
          phenol-lyases (EC 4.1.99.2) are found between trusted
          and noise cutoffs, but this model captures nearly all
          tryptophanases for which the leader peptide gene tnaC
          can be found upstream.
          Length = 467

 Score = 23.7 bits (51), Expect = 9.6
 Identities = 10/18 (55%), Positives = 11/18 (61%)

Query: 49 RAEEIENVKRTTSHLREE 66
          R   IE VKRTT   RE+
Sbjct: 8  RIRVIEPVKRTTRAYREK 25


>gnl|CDD|179861 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
          Length = 572

 Score = 23.8 bits (51), Expect = 9.9
 Identities = 13/32 (40%), Positives = 17/32 (53%)

Query: 60  TSHLREEITAIGKRLEKIEQQLADLELFINQK 91
           T+ L EE  AI    E+    L D+E +I QK
Sbjct: 348 TARLGEEGDAISFACERYAMSLPDIEAYIEQK 379


  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
   0.315    0.126    0.320 

Gapped
Lambda     K      H
   0.267   0.0691    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,441,858
Number of extensions: 79750
Number of successful extensions: 486
Number of sequences better than 10.0: 1
Number of HSP's gapped: 469
Number of HSP's successfully gapped: 176
Length of query: 94
Length of database: 5,994,473
Length adjustment: 62
Effective length of query: 32
Effective length of database: 4,654,777
Effective search space: 148952864
Effective search space used: 148952864
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.1 bits)