RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781158|ref|YP_003065571.1| peptidyl prolyl cis-trans
isomerase D signal peptide protein [Candidatus Liberibacter asiaticus
str. psy62]
         (631 letters)



>gnl|CDD|144291 pfam00639, Rotamase, PPIC-type PPIASE domain.  Rotamases increase
           the rate of protein folding by catalysing the
           interconversion of cis-proline and trans-proline.
          Length = 95

 Score = 35.3 bits (82), Expect = 0.053
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 7/79 (8%)

Query: 280 QKEADEAFQSLKKGK-KFIQLA----EEQGKSLSDISLGSFSKEYIPDVSLADSIFSLAK 334
           + +A+E  + L+ G+  F +LA    ++   + +   LG F++  +P     D++FSL K
Sbjct: 17  KAKAEEILEQLQSGEDTFAELAREYSDDCPSAANGGDLGWFTRGQLPPE-FEDAVFSL-K 74

Query: 335 KGDFTPVIHGSFGYVIAHV 353
           +G+ +  +   FGY I  V
Sbjct: 75  EGEISGPVKTPFGYHIIKV 93


>gnl|CDD|30890 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase
           (trigger factor) [Posttranslational modification,
           protein turnover, chaperones].
          Length = 441

 Score = 30.2 bits (68), Expect = 1.8
 Identities = 23/103 (22%), Positives = 52/103 (50%), Gaps = 2/103 (1%)

Query: 218 EKYKDNYRAPEYKRI-SYILFDVHEKEKKIEISNDELQAEYEKNKEKYFSPEIRTVEQLV 276
           E+ ++ ++    KR+   +L +   KE+K+E++ +E++AE E+   +Y   +   V +L 
Sbjct: 337 EELREEFKEEAEKRVKLGLLLEEIAKEEKLEVTEEEIKAEIEELARQYGGEQPEEVIKLY 396

Query: 277 FPNQKEADEAFQSLKKGKKF-IQLAEEQGKSLSDISLGSFSKE 318
           + NQ+  D     + + K   + LA ++  +  ++S      E
Sbjct: 397 YNNQELLDALKADILEEKAVDLLLANKKKVTEKEVSFEELMNE 439


>gnl|CDD|34165 COG4496, COG4496, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 100

 Score = 29.9 bits (67), Expect = 2.5
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 495 TAEEVSSKANQL-VLEYSKEGKNFRDIGKNLGASLLTTNQINRMDNENKFFGYDGISQVF 553
           T  E+ S A +L V +  KEG+ +RDI    GAS  T +++ R  N    +G DG + V 
Sbjct: 36  TINEIQSLAQRLQVAKMLKEGRTYRDIEDETGASTATISRVKRCLN----YGNDGYAMVL 91

Query: 554 S 554
            
Sbjct: 92  Q 92


>gnl|CDD|147705 pfam05698, Trigger_C, Bacterial trigger factor protein (TF)
           C-terminus.  In the E. coli cytosol, a fraction of the
           newly synthesized proteins requires the activity of
           molecular chaperones for folding to the native state.
           The major chaperones implicated in this folding process
           are the ribosome-associated Trigger Factor (TF), and the
           DnaK and GroEL chaperones with their respective
           co-chaperones. Trigger Factor is an ATP-independent
           chaperone and displays chaperone and
           peptidyl-prolyl-cis-trans-isomerase (PPIase) activities
           in vitro. It is composed of at least three domains, an
           N-terminal domain which mediates association with the
           large ribosomal subunit, a central substrate binding and
           PPIase domain with homology to FKBP proteins, and a
           C-terminal domain of unknown function. The positioning
           of TF at the peptide exit channel, together with its
           ability to interact with nascent chains as short as 57
           residues renders TF a prime candidate for being the
           first chaperone that binds to the nascent polypeptide
           chains. This family represents the C-terminal region of
           the protein.
          Length = 162

 Score = 29.5 bits (67), Expect = 2.6
 Identities = 15/78 (19%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 218 EKYKDNYRAPEYKRI-SYILFDVHEKEKKIEISNDELQAEYEKNKEKYFSPEIRTVEQLV 276
           E+ ++ ++    KR+   ++ +   KE+KIE++++E++ E E+   +Y        E   
Sbjct: 80  EELREEFKEEAEKRVKLGLILEEIAKEEKIEVTDEEIKEEIEELASQYGMEPEEVKEF-- 137

Query: 277 FPNQKEADEAFQSLKKGK 294
           +   ++     + L + K
Sbjct: 138 YKKNEQLSALKEDLLEEK 155


>gnl|CDD|99821 cd05778, DNA_polB_zeta_exo, inactive DEDDy 3'-5' exonuclease domain
           of eukaryotic DNA polymerase zeta, a family-B DNA
           polymerase.  The 3'-5' exonuclease domain of eukaryotic
           DNA polymerase zeta. DNA polymerase zeta is a family-B
           DNA polymerase which is distantly related to DNA
           polymerase delta. It plays a major role in translesion
           replication and the production of either spontaneous or
           induced mutations. In addition, DNA polymerase zeta also
           appears to be involved in somatic hypermutability in B
           lymphocytes, an important element for the production of
           high affinity antibodies in response to an antigen. The
           catalytic subunit contains both polymerase and 3'-5'
           exonuclease domains, but only exhibits polymerase
           activity. The DnaQ-like 3'-5' exonuclease domain
           contains three sequence motifs termed ExoI, ExoII and
           ExoIII, without the four conserved acidic residues that
           are crucial for metal binding and catalysis.
          Length = 231

 Score = 29.1 bits (66), Expect = 3.4
 Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 10/54 (18%)

Query: 187 FENRSVDYIVLNNRHVPAIADPSNAVLTQWFEKYKDN--YRAPEY--KRISYIL 236
            EN  V Y VL+ R    I   SN  LT+W++    +  +R  EY  KR+   L
Sbjct: 180 LEN--VVYHVLHQR----IPLYSNKTLTEWYKSGSASERWRVLEYYLKRVRLNL 227


>gnl|CDD|145500 pfam02388, FemAB, FemAB family.  The femAB operon codes for two
           nearly identical approximately 50-kDa proteins involved
           in the formation of the Staphylococcal pentaglycine
           interpeptide bridge in peptidoglycan. These proteins are
           also considered as a factor influencing the level of
           methicillin resistance.
          Length = 407

 Score = 28.8 bits (65), Expect = 4.2
 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 5/89 (5%)

Query: 217 FEKYKDNYRAPEYKRISYILFD-----VHEKEKKIEISNDELQAEYEKNKEKYFSPEIRT 271
           +EK  D +       ++Y+ FD     + +K +K+E    +L+A+ EKN       ++  
Sbjct: 219 YEKLLDTFGDKAEFTLAYLNFDEYLDELQQKLEKLEKDLAKLEADLEKNPNSKKKNKLAE 278

Query: 272 VEQLVFPNQKEADEAFQSLKKGKKFIQLA 300
           +EQ +   +K  DEA + + K    + LA
Sbjct: 279 LEQQLASLEKRIDEAKELIAKYGNEVPLA 307


>gnl|CDD|145498 pfam02383, Syja_N, SacI homology domain.  This Pfam family
           represents a protein domain which shows homology to the
           yeast protein SacI. The SacI homology domain is most
           notably found at the amino terminal of the inositol
           5'-phosphatase synaptojanin.
          Length = 302

 Score = 28.7 bits (65), Expect = 5.4
 Identities = 12/38 (31%), Positives = 19/38 (50%)

Query: 208 PSNAVLTQWFEKYKDNYRAPEYKRISYILFDVHEKEKK 245
            S   L++ +E+  +    PE K+I Y  FD H + K 
Sbjct: 260 GSEKKLSEAYEEAINYLNLPENKKIKYTWFDFHAECKG 297


>gnl|CDD|37128 KOG1917, KOG1917, KOG1917, Membrane-associated hematopoietic
           protein [General function prediction only].
          Length = 1125

 Score = 28.4 bits (63), Expect = 5.5
 Identities = 15/78 (19%), Positives = 35/78 (44%), Gaps = 9/78 (11%)

Query: 288 QSLKKGKKFIQLAEEQGKSLSDISLGSFSKEYIPDVSLADSIFSLAK------KGDFTPV 341
           +S +K +K + + ++   +L+++    F+  Y+P + + +  F+  +      +G F   
Sbjct: 660 ESYRKNRKSLTMLDKLHTALTELC---FALNYVPPICVWEHTFAPREYLRQHLEGRFKRR 716

Query: 342 IHGSFGYVIAHVSNIKPS 359
           + G   Y        KPS
Sbjct: 717 LVGMLMYNQTTQEIAKPS 734


>gnl|CDD|37099 KOG1888, KOG1888, KOG1888, Putative phosphoinositide phosphatase
           [Lipid transport and metabolism].
          Length = 868

 Score = 28.4 bits (63), Expect = 5.7
 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 5/69 (7%)

Query: 181 QAKRFYFENRSVDY---IVLNNRHVPAIADPSNAVLTQWFEKYKD--NYRAPEYKRISYI 235
           +    +F+N    Y   I++ N        P  ++L + FE   D  N   P   R+ YI
Sbjct: 322 ETAALHFDNLVQRYGNPIIILNLIKTNEKRPRESILREEFENAIDYLNQFLPPENRLKYI 381

Query: 236 LFDVHEKEK 244
            +D+H+  K
Sbjct: 382 HWDMHKHSK 390


>gnl|CDD|30630 COG0282, ackA, Acetate kinase [Energy production and conversion].
          Length = 396

 Score = 28.2 bits (63), Expect = 7.1
 Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 8/47 (17%)

Query: 126 HGKDNKFSHDVFVSRLAREGINEKEYIDHYTKMLSRTDVVGMFVGGM 172
            G + K + D+FV R+A+       YI  Y   L   D + +F  G+
Sbjct: 291 EGNEAKLALDMFVYRIAK-------YIGSYAAALGGLDAL-VFTAGI 329


>gnl|CDD|36377 KOG1162, KOG1162, KOG1162, Predicted small molecule transporter
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 617

 Score = 27.9 bits (62), Expect = 9.6
 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 10/82 (12%)

Query: 215 QWFEKYKDNYRAPEYKRISYILFDVHE-KEKKIEISNDELQAEYEKNKEKYFS---PEIR 270
           +W + Y D      YK +  +L ++ E K    E +   +  E  + +E +F     E+ 
Sbjct: 14  EWRQAYID------YKYLKKLLKEIIENKPSSEETTFLMVSEEGGEFEEVFFRRLDEELN 67

Query: 271 TVEQLVFPNQKEADEAFQSLKK 292
            V +      KEA E  + L K
Sbjct: 68  KVNKFYKEKVKEAREEAEELNK 89


  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
   0.317    0.135    0.381 

Gapped
Lambda     K      H
   0.267   0.0790    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 7,510,755
Number of extensions: 410531
Number of successful extensions: 1220
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1220
Number of HSP's successfully gapped: 33
Length of query: 631
Length of database: 6,263,737
Length adjustment: 100
Effective length of query: 531
Effective length of database: 4,102,837
Effective search space: 2178606447
Effective search space used: 2178606447
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 (21.7 bits)
S2: 60 (26.8 bits)