RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780291|ref|YP_003064704.1| hypothetical protein
CLIBASIA_00880 [Candidatus Liberibacter asiaticus str. psy62]
         (475 letters)



>gnl|CDD|179784 PRK04204, PRK04204, RNA 3'-terminal-phosphate cyclase; Provisional.
          Length = 343

 Score = 30.6 bits (70), Expect = 0.92
 Identities = 8/16 (50%), Positives = 10/16 (62%)

Query: 420 TGRPVRVYNINKNSKN 435
           TG+P R+ NI  N  N
Sbjct: 27  TGKPFRITNIRANRPN 42


>gnl|CDD|150358 pfam09669, Phage_pRha, Phage regulatory protein Rha (Phage_pRha).
           Members of this protein family are found in temperate
           phage and bacterial prophage regions. Members include
           the product of the rha gene of the lambdoid phage
           phi-80, a late operon gene. The presence of this gene
           interferes with infection of bacterial strains that lack
           integration host factor (IHF), which regulates the rha
           gene. It is suggested that Rha is a phage regulatory
           protein.
          Length = 86

 Score = 30.2 bits (69), Expect = 1.2
 Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 3/31 (9%)

Query: 412 PESYIKDSTGRPVRVYNINKNSKNEFILLEM 442
            ES   DS GR   +Y +    K+ F+LL M
Sbjct: 34  IESSYTDSRGRKYPMYLLT---KDGFMLLVM 61


>gnl|CDD|182838 PRK10919, PRK10919, ATP-dependent DNA helicase Rep; Provisional.
          Length = 672

 Score = 29.8 bits (67), Expect = 1.4
 Identities = 17/34 (50%), Positives = 21/34 (61%), Gaps = 4/34 (11%)

Query: 387 QKRMFEKFLTQSKISTIFT--TRFTSSPESYIKD 418
           Q R+FEKFL Q++I    +  T F S PE  IKD
Sbjct: 354 QSRVFEKFLMQNRIPYKISGGTSFFSRPE--IKD 385


>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 = 30.0 bits (69), Expect = 1.5
 Identities = 9/41 (21%), Positives = 21/41 (51%)

Query: 17 GNITILTAIIIPLIITLITISTTCANILYHRASIEASADEA 57
          G   +  A+++P+++ L+        + Y R  ++ +A EA
Sbjct: 1  GAAAVEFALVLPVLLLLLFGIVELGRLFYARQVLQNAAREA 41


>gnl|CDD|162399 TIGR01525, ATPase-IB_hvy, heavy metal translocating P-type ATPase. 
           This alignment encompasses two equivalog models for the
           copper and cadmium-type heavy metal transporting P-type
           ATPases (TIGR01511 and TIGR01512) as well as those
           species which score ambiguously between both models. For
           more comments and references, see the files on TIGR01511
           and 01512.
          Length = 556

 Score = 29.5 bits (67), Expect = 1.8
 Identities = 35/197 (17%), Positives = 66/197 (33%), Gaps = 40/197 (20%)

Query: 9   KTIFLSKKGNIT----ILTAIIIPLIITLITISTTCANILYHRASIEASADEALNHGIVL 64
           KT+   K G +T     +  +     +   +IS     +L   A++E S+   L   IV 
Sbjct: 247 KTVVFDKTGTLTTGKPTVVDV---EPLDDASISEEE--LLALAAALEQSSSHPLARAIVR 301

Query: 65  LCKDSDLTPQDITPPVLKDLET---SLIKNDFSIKEAAQIKKESSINYQGKIPLSQGTYL 121
             K      + +  P  +D+E      ++     +E  +I     +    +   +    L
Sbjct: 302 YAKK-----RGLELPKQEDVEEVPGKGVEATVDGQEEVRIGNPRLLELAAEPISASPDLL 356

Query: 122 NLHAVYHVPLNSLERILLPHKQNMDIVVDVNKILNCHHKGIAVIADPWYKADTPMFVEAI 181
           N        +  +                     +    G+  + D   + +     EAI
Sbjct: 357 NEGESQGKTVVFVAV-------------------DGELLGVIALRDQ-LRPEAK---EAI 393

Query: 182 NSLKSSKNIILGILTGD 198
            +LK +  I L +LTGD
Sbjct: 394 AALKRAGGIKLVMLTGD 410


>gnl|CDD|163249 TIGR03399, RNA_3prim_cycl, RNA 3'-phosphate cyclase.  Members of
           this protein family are RNA 3'-phosphate cyclase
           (6.5.1.4), an enzyme whose function is conserved from E.
           coli to human. The modification this enzyme performs
           enables certain RNA ligations to occur, although the
           full biological roll for this enzyme is not fully
           described. This model separates this enzyme from a
           related protein, present only in eukaryotes, localized
           to the nucleolus, and involved in ribosomal
           modification.
          Length = 326

 Score = 28.8 bits (65), Expect = 2.8
 Identities = 9/16 (56%), Positives = 11/16 (68%)

Query: 420 TGRPVRVYNINKNSKN 435
           TG+PVR+YNI  N   
Sbjct: 25  TGKPVRIYNIRANRPK 40


>gnl|CDD|182203 PRK10034, PRK10034, fructuronate transporter; Provisional.
          Length = 447

 Score = 28.7 bits (64), Expect = 3.1
 Identities = 13/22 (59%), Positives = 17/22 (77%)

Query: 23  TAIIIPLIITLITISTTCANIL 44
           T+I++PLI  +I ISTT ANI 
Sbjct: 227 TSILVPLIPAIIMISTTIANIW 248


>gnl|CDD|130575 TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type
           ATPase.  One member from Halobacterium is annotated as
           "molybdenum-binding protein" although no evidence can be
           found for this classification.
          Length = 562

 Score = 28.4 bits (64), Expect = 3.7
 Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 9/52 (17%)

Query: 147 IVVDVNKILNCHHKGIAVIADPWYKADTPMFVEAINSLKSSKNIILGILTGD 198
           ++V VN        G+  + D   + +     E I +LK  + I   +LTGD
Sbjct: 388 VLVAVNG----ELAGVFALEDQ-LRPEA---KEVIQALKR-RGIEPVMLTGD 430


>gnl|CDD|182907 PRK11023, PRK11023, outer membrane lipoprotein; Provisional.
          Length = 191

 Score = 28.1 bits (63), Expect = 5.2
 Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 3/36 (8%)

Query: 83  DLETSLIKNDFSIKEAAQIKKESSIN---YQGKIPL 115
           D  T  ++ + ++ +  QIKKE+ IN   YQGK+ L
Sbjct: 46  DDGTLELRVNNALSKDEQIKKEARINVTAYQGKVLL 81


>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
           domain fusion protein; Reviewed.
          Length = 725

 Score = 27.7 bits (62), Expect = 6.1
 Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 4/34 (11%)

Query: 358 IRDDVFQAQ----REGKYIILFADDIDRFSSIDQ 387
           +R +V +A+    R GK  ILF D++ RF+   Q
Sbjct: 93  LRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQ 126


>gnl|CDD|128865 smart00602, VPS10, VPS10 domain. 
          Length = 612

 Score = 27.8 bits (62), Expect = 6.3
 Identities = 8/50 (16%), Positives = 16/50 (32%), Gaps = 3/50 (6%)

Query: 298 SQSYSWNIDNVHFIQANYSMFHSVYFNDEWSNIFTVAVPEHISKQDLPSH 347
           S  ++ + +    I     +F S   +DE  +     +P       L   
Sbjct: 38  SDFFNSSANKFKTILVKGYIFIS---SDEGKSFQKFTLPFPPLPSLLYHP 84


>gnl|CDD|181587 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
          Length = 306

 Score = 27.9 bits (63), Expect = 6.4
 Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 19/44 (43%)

Query: 353 EISQWIRDDVFQAQREGKYIILFADDIDRFSSIDQKRMFEKFLT 396
           ++S W+RD+V          IL            Q RM E+  T
Sbjct: 230 QMSSWVRDEVLGV-------IL------------QYRMQEELPT 254


>gnl|CDD|183981 PRK13333, PRK13333, pantothenate kinase; Reviewed.
          Length = 206

 Score = 27.6 bits (62), Expect = 6.5
 Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 9/60 (15%)

Query: 393 KFLTQSKISTIFTTRFTSSPESYIKDSTGRPVRVYNINKNSKNEFILLEMTPHYINVTAY 452
            F    KI ++    F       I         +Y I+ N + E  LL+  P+ IN+  Y
Sbjct: 12  HFYQNGKIFSLSIEEFKRF---KIDQ------EIYYISVNEELEKKLLKCYPNAINLEPY 62


>gnl|CDD|181028 PRK07559, PRK07559, 2'-deoxycytidine 5'-triphosphate deaminase;
           Provisional.
          Length = 365

 Score = 27.6 bits (62), Expect = 6.9
 Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 2/29 (6%)

Query: 112 KIPLSQGTYLNLHAVYHVPLNSLERILLP 140
           +I L+ G  L    VY VPL  LE + LP
Sbjct: 75  EIDLTDGAVLETGCVYIVPL--LESLALP 101


>gnl|CDD|171504 PRK12445, PRK12445, lysyl-tRNA synthetase; Reviewed.
          Length = 505

 Score = 27.7 bits (61), Expect = 7.0
 Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 411 SPESYIKD-STGRPVRVYNINKNSKNEFILLEMTPHYINVTAY 452
           +PE Y+K    G   RV+ IN+N +NE I +   P +  +  Y
Sbjct: 239 APELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFTMMELY 281


>gnl|CDD|177912 PLN02272, PLN02272, glyceraldehyde-3-phosphate dehydrogenase.
          Length = 421

 Score = 27.5 bits (61), Expect = 7.1
 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 7/39 (17%)

Query: 158 HHKGIA---VIADPWYKADTPMFVEAIN--SLKSSKNII 191
           H KG A   VI+ P   AD PMFV  +N  + K + NI+
Sbjct: 194 HLKGGAKKVVISAP--SADAPMFVVGVNEKTYKPNMNIV 230


>gnl|CDD|128867 smart00604, MD, MD domain. 
          Length = 145

 Score = 27.5 bits (61), Expect = 8.2
 Identities = 9/50 (18%), Positives = 16/50 (32%), Gaps = 2/50 (4%)

Query: 234 RPCRDPYTL--TPSIYGCAFIAINDISQQINDHYPQIKSIKEFNGDSQRY 281
           R C     L       GCA+  ++      +     I  + E   + +R 
Sbjct: 96  RFCTYAPVLERLSLTDGCAYEFVSTSDFSCDYFVVLIDGVDENGYNFRRT 145


>gnl|CDD|162366 TIGR01448, recD_rel, helicase, putative, RecD/TraA family.  This
           model describes a family similar to RecD, the
           exodeoxyribonuclease V alpha chain of TIGR01447. Members
           of this family, however, are not found in a context of
           RecB and RecC and are longer by about 200 amino acids at
           the amino end. Chlamydia muridarum has both a member of
           this family and a RecD.
          Length = 720

 Score = 27.1 bits (60), Expect = 9.6
 Identities = 8/52 (15%), Positives = 18/52 (34%), Gaps = 4/52 (7%)

Query: 214 IYSLKFPFFRGLGSQEYIGNRP----CRDPYTLTPSIYGCAFIAINDISQQI 261
           +  L           ++          +DPY L   + G  F+  + ++Q +
Sbjct: 150 LQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQAL 201


  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
   0.319    0.135    0.395 

Gapped
Lambda     K      H
   0.267   0.0747    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,655,801
Number of extensions: 489117
Number of successful extensions: 1029
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1028
Number of HSP's successfully gapped: 30
Length of query: 475
Length of database: 5,994,473
Length adjustment: 97
Effective length of query: 378
Effective length of database: 3,898,497
Effective search space: 1473631866
Effective search space used: 1473631866
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.5 bits)