RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780548|ref|YP_003064961.1| translocation protein TolB
[Candidatus Liberibacter asiaticus str. psy62]
         (447 letters)



>gnl|CDD|31165 COG0823, TolB, Periplasmic component of the Tol biopolymer
           transport system [Intracellular trafficking and
           secretion].
          Length = 425

 Score =  249 bits (637), Expect = 9e-67
 Identities = 142/431 (32%), Positives = 213/431 (49%), Gaps = 12/431 (2%)

Query: 20  LLVLIGGFFPTSIHAFVKVATNSANYSPVSIAFTKFVSIDE--LGGKVSEVVSKDLQRSD 77
           +L+ I   F  +  A V +  NS   SP+ IA   F        G  +S +V+ DL+ S 
Sbjct: 3   ILLAITLVFQVTA-ALVLIVINSGVDSPLPIAVVSFSPDGGALPGEDISGIVAADLKASG 61

Query: 78  VFNLISQDSFKQKITNPDSIPRFQDWNSLGAQVLVTGRVIKEGKDRLRVEFRLWDVKDRK 137
            F  + +  + +  +   S P   DW +LGA  +V G+V        R  F+L+D     
Sbjct: 62  KFIPLDRAGYIELPSGA-SEPLPPDWKALGADAVVLGQVTPSPDGSYRSSFQLFDTSTGF 120

Query: 138 QIIGKKFFSSPASWRKIAHTISDDIYQSITGEKGDFNSRILFVSESVVSGIIKNSLCVMD 197
           Q++G     +    R+ AHTI+D IY+ +TG KG F++RI +V+ES    +    L + D
Sbjct: 121 QLLGNSLVVTALLLRRAAHTIADAIYEKLTGIKGAFDTRIAYVAESDGGPLPYE-LALGD 179

Query: 198 RDGANIRYLTPSRDQILFEPRFSPNQQKVAYATYDDEDILRVYLMDTRIDRAPKRIGNFR 257
            DG N + LT S   IL  P +SP+ +K+AY +++     R+Y +D    + P  I NF 
Sbjct: 180 YDGYNQQKLTDSGSLILT-PAWSPDGKKLAYVSFELGGCPRIYYLDLNTGKRP-VILNFN 237

Query: 258 SMILAPRFSSNGKRALISVQKDEAMDIYSVDLQSNATERLTNTLFINISASYSPDSSQIV 317
               AP FS +G +   S  +D + DIY +DL      RLTN   IN S S+SPD S+IV
Sbjct: 238 GNNGAPAFSPDGSKLAFSSSRDGSPDIYLMDLDGKNLPRLTNGFGINTSPSWSPDGSKIV 297

Query: 318 FESDREGKEQLYVMQSNGSDQKRISQDKEASYFDPVWSPQGDLIAFTKFSGEKFAIGVMK 377
           F SDR G+ Q+Y+    GS   R++        +PVWSP GD I F   SG ++ I    
Sbjct: 298 FTSDRGGRPQIYLYDLEGSQVTRLT-FSGGGNSNPVWSPDGDKIVFESSSGGQWDIDKND 356

Query: 378 -KDGSQERLLVEDSNLQAPTWSPSGRSLIFSRKKDGDTGSKLYSIDLNGRNETLINTP-A 435
              G + R+L      ++P+W+P+GR ++FS       GS L  + L+GR    +     
Sbjct: 357 LASGGKIRILTSTYLNESPSWAPNGRMIMFS--SGQGGGSVLSLVSLDGRVSRPLPLADG 414

Query: 436 YASDPQWVGFM 446
               P W   +
Sbjct: 415 DVRVPAWSPVL 425


>gnl|CDD|146599 pfam04052, TolB_N, TolB amino-terminal domain.  TolB is an
           essential periplasmic component of the tol-dependent
           translocation system. This function of this amino
           terminal domain is uncertain.
          Length = 106

 Score = 90.8 bits (226), Expect = 7e-19
 Identities = 38/101 (37%), Positives = 50/101 (49%), Gaps = 5/101 (4%)

Query: 42  SANYSPVSIAFTKFV---SIDELGGKVSEVVSKDLQRSDVFNLISQDSFKQKITNPDSIP 98
                P+ IA   F       EL   +SEV++ DL RS +F  I   +F    T+ +S  
Sbjct: 8   GGVDRPLPIAVVPFAGEGGAAELPEDISEVIAADLARSGLFRPIDPSAFPSSPTS-NSEV 66

Query: 99  RFQDWNSLGAQVLVTGRVIKEGKDRLRVEFRLWDVKDRKQI 139
            F DW +LGA  LV G V     D L VEFRL+DV   +Q+
Sbjct: 67  DFADWRALGADALVVGSV-TSSGDGLTVEFRLYDVFSGQQL 106


>gnl|CDD|31695 COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases
           [Amino acid transport and metabolism].
          Length = 620

 Score = 53.7 bits (128), Expect = 9e-08
 Identities = 36/251 (14%), Positives = 76/251 (30%), Gaps = 34/251 (13%)

Query: 199 DGANIRYLTPSRDQILFEPRFSPNQQKVAYATYDDEDILRVYLMDTRIDRAPKRIGNFRS 258
           DG  +R LT      + E R+SP+   +A+ + D   + ++YL+D         I     
Sbjct: 49  DGKTVRLLTFGGG--VSELRWSPDGSVLAFVSTDGGRVAQLYLVDVG-----GLITKTAF 101

Query: 259 MILAPRFSSNGKRALISVQKDEAMDIYSVDLQSNATERLTNTLFINISASYSPDSSQIVF 318
            +   R+S +G R                 L +    +               D   + F
Sbjct: 102 GVSDARWSPDGDR--------------IAFLTAEGASKRDG------GDHLFVDRLPVWF 141

Query: 319 ESDREGKEQLYVMQSNGSDQKRISQDKEASYFDPVWSPQGDLIAFTKFSGEKF-----AI 373
           +     +  LYV+      +                   G L+A  +   +         
Sbjct: 142 DGRGGERSDLYVVDIES--KLIKLGLGNLDVVSFATDGDGRLVASIRLDDDADPWVTNLY 199

Query: 374 GVMKKDGSQERLLVEDSNLQAPTWSPSGRSLIFSRKKDGDTGSKLYSIDLNGRNETLINT 433
            +++ +G  E L   + ++    +   G+S+     +     ++   I L       ++ 
Sbjct: 200 VLIEGNGELESLTPGEGSISKLAFDADGKSIALLGTESDRGLAEGDFILLLDGELGEVDG 259

Query: 434 PAYASDPQWVG 444
              + D     
Sbjct: 260 DLSSGDDTRGA 270



 Score = 36.7 bits (84), Expect = 0.014
 Identities = 28/96 (29%), Positives = 38/96 (39%), Gaps = 8/96 (8%)

Query: 351 DPVWSPQGDLIAFTK----FSGEKFAIGVMKKDGSQERLLVEDSNLQAPTWSPSGRSLIF 406
           DP  SP G  +A+      F    +   +   DG   RLL     +    WSP G  L F
Sbjct: 17  DPRVSPPGGRLAYILTGLDFLKPLYKSSLWVSDGKTVRLLTFGGGVSELRWSPDGSVLAF 76

Query: 407 SRKKDGDTGSKLYSIDLNGRNETLINTPAYASDPQW 442
               DG   ++LY +D+ G       T    SD +W
Sbjct: 77  VS-TDGGRVAQLYLVDVGGLIT---KTAFGVSDARW 108


>gnl|CDD|144507 pfam00930, DPPIV_N, Dipeptidyl peptidase IV (DPP IV) N-terminal
           region.  This family is an alignment of the region to
           the N-terminal side of the active site. The Prosite
           motif does not correspond to this Pfam entry.
          Length = 349

 Score = 45.8 bits (109), Expect = 2e-05
 Identities = 29/124 (23%), Positives = 46/124 (37%), Gaps = 27/124 (21%)

Query: 266 SSNGKRALISVQKDE------AMDIYSVDLQSNATERLTNTLFINISASYSPDSSQIVFE 319
           S +GK  L++   ++          Y  DL++   E L         A +SPD  ++ + 
Sbjct: 1   SPDGKYLLLATNYEKIWRHSYTASYYIYDLETGTVEPLPPGEGKIQYAKWSPDGHKLAYV 60

Query: 320 SDREGKEQLYVMQSNGSDQKRISQDKEASYF----DPV-------------WSPQGDLIA 362
            D      LYV +     + +I+ D     F    D V             WSP G  +A
Sbjct: 61  RDNN----LYVRELATGKETQITSDGSNGIFNGLADWVYEEEVFGSNSAYWWSPDGSRLA 116

Query: 363 FTKF 366
           F +F
Sbjct: 117 FLRF 120



 Score = 34.2 bits (79), Expect = 0.070
 Identities = 14/66 (21%), Positives = 34/66 (51%), Gaps = 5/66 (7%)

Query: 282 MDIYSVDLQSNATERL---TNTLFINISAS--YSPDSSQIVFESDREGKEQLYVMQSNGS 336
           +D+  VD ++  T  L   T+  ++ +     +  D S  ++ S+R+G + LY+   +G 
Sbjct: 208 LDLVLVDTETGRTVVLLEETSDGWVELHQDPVFLRDGSGFLWISERDGYKHLYLYDLDGK 267

Query: 337 DQKRIS 342
             ++++
Sbjct: 268 LPRQLT 273



 Score = 33.4 bits (77), Expect = 0.13
 Identities = 11/34 (32%), Positives = 17/34 (50%)

Query: 284 IYSVDLQSNATERLTNTLFINISASYSPDSSQIV 317
           +Y V L     + LT+    + SAS+SP+    V
Sbjct: 306 LYRVSLDGGEPQCLTDESGDHDSASFSPNGKYYV 339



 Score = 28.0 bits (63), Expect = 5.6
 Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 6/54 (11%)

Query: 378 KDGSQERLLVEDSNLQAPTWSPSGRSLIFSRKKDGDTGSKLYSIDLNGRNETLI 431
           + G+ E L   +  +Q   WSP G  L + R  +      LY  +L    ET I
Sbjct: 31  ETGTVEPLPPGEGKIQYAKWSPDGHKLAYVRDNN------LYVRELATGKETQI 78


>gnl|CDD|34554 COG4946, COG4946, Uncharacterized protein related to the
           periplasmic component of the Tol biopolymer transport
           system [Function unknown].
          Length = 668

 Score = 37.6 bits (87), Expect = 0.008
 Identities = 31/145 (21%), Positives = 58/145 (40%), Gaps = 7/145 (4%)

Query: 264 RFSSNGKRALISVQKDEAMDIYSVDLQSNATERLTNTLFINISASYSPDSSQIVFESDRE 323
           R   + +  +I     + + IY  D      +R+   L    +   SPD  ++V  +DR 
Sbjct: 366 RIQVDPEGDVIGTNDGDKLGIY--DKDGGEVKRIEKDLGNIEAVKVSPDGKKVVVANDRF 423

Query: 324 GKEQLYVMQSNGSDQKRISQDKEASYFDPVWSPQGDLIAFTKFSG-EKFAIGVMKKDGSQ 382
              +L+V+  +  + + I + +     D  W P    IA+    G    +I +   DG +
Sbjct: 424 ---ELWVIDIDNGNVRLIDKSEYGLITDFDWHPNSRWIAYAFPEGYYTQSIKLYDMDGGK 480

Query: 383 E-RLLVEDSNLQAPTWSPSGRSLIF 406
              +    +   +P + P GR L F
Sbjct: 481 IYDVTTPTAYDFSPAFDPDGRYLYF 505



 Score = 36.8 bits (85), Expect = 0.012
 Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 8/90 (8%)

Query: 283 DIYSVDLQSNATERLTNTLFINISASYSPDSSQIVFESDREGKE----QLYVMQSNGSDQ 338
           D++   L+     R+T+ L +  +  +SPD  ++ F     G       LYV+ S   + 
Sbjct: 60  DLWEYSLKDGKPLRITSGLGVVNNPKFSPDGRKVAFSRVMLGSSLQTADLYVVPSEDGEA 119

Query: 339 KRISQDKEASYFDPV--WSPQGDLIAFTKF 366
           KRI+       F  V  W P G++I  T F
Sbjct: 120 KRITY--FGRRFTRVAGWIPDGEIIVSTDF 147



 Score = 35.3 bits (81), Expect = 0.034
 Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 247 DRAPKRIGNFRSMILAPRFSSNGKRALISV----QKDEAMDIYSVDLQSNATERLT--NT 300
           D  P RI +   ++  P+FS +G++   S        +  D+Y V  +    +R+T    
Sbjct: 68  DGKPLRITSGLGVVNNPKFSPDGRKVAFSRVMLGSSLQTADLYVVPSEDGEAKRITYFGR 127

Query: 301 LFINISASYSPDSSQIV 317
            F  + A + PD   IV
Sbjct: 128 RFTRV-AGWIPDGEIIV 143



 Score = 30.7 bits (69), Expect = 0.77
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 2/51 (3%)

Query: 377 KKDGSQERLLVEDSNLQAPTWSPSGRSLIFSR--KKDGDTGSKLYSIDLNG 425
            KDG   R+      +  P +SP GR + FSR         + LY +    
Sbjct: 66  LKDGKPLRITSGLGVVNNPKFSPDGRKVAFSRVMLGSSLQTADLYVVPSED 116


>gnl|CDD|37350 KOG2139, KOG2139, KOG2139, WD40 repeat protein [General function
           prediction only].
          Length = 445

 Score = 33.5 bits (76), Expect = 0.12
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 354 WSPQGDLIAFTKFSGEKFAIGVMKKDGSQERLLVEDSNLQAPTWSPSGRSLIFSRKKDGD 413
           WSP GD++         F +    +  ++ER ++    +Q   WSP G  L+F+      
Sbjct: 246 WSPDGDVLFAATCDA-VFRLWQENQSWTKERWILGSGRVQTACWSPCGSFLLFACSGS-- 302

Query: 414 TGSKLYSIDLNGR 426
              +LYS+  +G 
Sbjct: 303 --PRLYSLTFDGE 313


>gnl|CDD|36659 KOG1446, KOG1446, KOG1446, Histone H3 (Lys4) methyltransferase
           complex and RNA cleavage factor II complex, subunit SWD2
           [RNA processing and modification, Chromatin structure
           and dynamics, Posttranslational modification, protein
           turnover, chaperones].
          Length = 311

 Score = 30.2 bits (68), Expect = 1.2
 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 264 RFSSNGKRALISVQKDEA--MDIYSVDLQSNATERLTNTLFINISASYSPDSSQIVFESD 321
            FS +GK  L+S        +D +   ++S  +    N   + +SA+++PDS  ++  SD
Sbjct: 194 EFSPDGKSILLSTNASFIYLLDAFDGTVKSTFSG-YPNAGNLPLSATFTPDSKFVLSGSD 252


>gnl|CDD|38769 KOG3561, KOG3561, KOG3561, Aryl-hydrocarbon receptor nuclear
           translocator [Transcription].
          Length = 803

 Score = 30.1 bits (67), Expect = 1.4
 Identities = 24/108 (22%), Positives = 40/108 (37%), Gaps = 8/108 (7%)

Query: 176 RILFVSESVVSGIIKNSLCVMDRDGANIRYLTPSRDQILFEPRFSPNQQKVAYATYDDED 235
           RI++VSESV S +        D  G ++  +    D      + SP   +  +       
Sbjct: 116 RIVYVSESVTSVL---GYLQSDLMGQSLYDILHPLDNDKPREQLSPRSNEHTFNCR---- 168

Query: 236 ILRVYLMDTRIDRAPKRIGNFRSMILAPRFSSNGKRALISVQKDEAMD 283
            L         + A K  GNF+    +   S  G ++ I  Q+ +A  
Sbjct: 169 -LLDGKTGPPPEEAVKFYGNFQCFTNSQPKSIEGFQSTICRQRRKAEG 215


>gnl|CDD|35574 KOG0353, KOG0353, KOG0353, ATP-dependent DNA helicase [General
           function prediction only].
          Length = 695

 Score = 29.0 bits (64), Expect = 2.5
 Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 2/45 (4%)

Query: 313 SSQIVFESDREGKEQLYVMQSNGSDQKRISQDKEASYFDPVWSPQ 357
           SS +  E    G ++LY M    +D  +  + K A +FD  W P+
Sbjct: 473 SSMVQME--NTGIQKLYEMVRYAADISKCRRVKLAEHFDEAWEPE 515


>gnl|CDD|143923 pfam00155, Aminotran_1_2, Aminotransferase class I and II. 
          Length = 351

 Score = 29.2 bits (66), Expect = 2.5
 Identities = 5/46 (10%), Positives = 11/46 (23%), Gaps = 8/46 (17%)

Query: 147 SPASWRKIA--------HTISDDIYQSITGEKGDFNSRILFVSESV 184
                 K+           + D+ Y        D  +    ++E  
Sbjct: 154 PLEELEKLLDLAKEHNILLLVDEAYAGFVFGSPDAVATRALLAEGP 199


>gnl|CDD|35514 KOG0293, KOG0293, KOG0293, WD40 repeat-containing protein [Function
           unknown].
          Length = 519

 Score = 29.2 bits (65), Expect = 2.6
 Identities = 24/112 (21%), Positives = 48/112 (42%), Gaps = 3/112 (2%)

Query: 206 LTPSRDQILFEPRFSPNQQKVAYATYDDEDILRVYLMDTRIDRAPKRIGNFRSMILAPRF 265
           L    D++ F  +FS N + +A A+ D   I+ + + D         +G+ +  +    +
Sbjct: 220 LQDHTDEVWF-LQFSHNGKYLASASKDSTAIIWIVVYDVHFKLKKTLVGHSQP-VSYIMW 277

Query: 266 SSNGKRALISVQKDEAMDIYSVDLQSNATERLTNTLFINISASYSPDSSQIV 317
           S +  R L++   DE + ++ VD         +   F   S ++ PD  + V
Sbjct: 278 SPD-DRYLLACGFDEVLSLWDVDTGDLRHLYPSGLGFSVSSCAWCPDGFRFV 328


>gnl|CDD|33024 COG3211, PhoX, Predicted phosphatase [General function prediction
           only].
          Length = 616

 Score = 28.8 bits (64), Expect = 3.3
 Identities = 26/117 (22%), Positives = 44/117 (37%), Gaps = 16/117 (13%)

Query: 319 ESDREGKEQLYVMQSNGSDQK-----RISQDKEASYFDPVWSPQGDLIAFTKFSGEK--- 370
            +D +    L+V   N S  +      I+ +   S  +  + P G L   T  SG     
Sbjct: 467 HTDTKFTWDLFVEAGNPSVLEGGASANINANWFNSPDNLAFDPWGRLWIQTDGSGSTLRN 526

Query: 371 FAIGVMKKD------GSQERLLVED--SNLQAPTWSPSGRSLIFSRKKDGDTGSKLY 419
              GV +        G+ +R L          P +SP G++L  + +  G+TG+   
Sbjct: 527 RFRGVTQMLTPDPKTGTIKRFLTGPIGCEFTGPCFSPDGKTLFVNVQHPGETGTTTN 583


>gnl|CDD|107209 cd06448, L-Ser-dehyd, Serine dehydratase is a pyridoxal phosphate
           (PLP)-dependent enzyme which catalyzes the conversion of
           L- , D-serine, or L-threonine to pyruvate/ketobutyrate
           and ammonia..
          Length = 316

 Score = 28.4 bits (64), Expect = 3.8
 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 3/39 (7%)

Query: 90  KITNPDSIPRFQDWNSLGAQVLVTGRVIKEGKDRLRVEF 128
           + T P  + + +D    GA V+V G+V  E  + LR E 
Sbjct: 83  ESTKPRVVEKLRD---EGATVVVHGKVWWEADNYLREEL 118


>gnl|CDD|100087 cd03085, PGM1, Phosphoglucomutase 1 (PGM1) catalyzes the
           bidirectional interconversion of glucose-1-phosphate
           (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose
           1,6-diphosphate intermediate, an important metabolic
           step in prokaryotes and eukaryotes. In one direction,
           G-1-P produced from sucrose catabolism is converted to
           G-6-P, the first intermediate in glycolysis. In the
           other direction, conversion of G-6-P to G-1-P generates
           a substrate for synthesis of UDP-glucose which is
           required for synthesis of a variety of cellular
           constituents including cell wall polymers and
           glycoproteins. The PGM1 family also includes a
           non-enzymatic PGM-related protein (PGM-RP) thought to
           play a structural role in eukaryotes, as well as
           pp63/parafusin, a phosphoglycoprotein that plays an
           important role in calcium-regulated exocytosis in
           ciliated protozoans. PGM1 belongs to the
           alpha-D-phosphohexomutase superfamily which includes
           several related enzymes that catalyze a reversible
           intramolecular phosphoryl transfer on their sugar
           substrates. Other members of this superfamily include
           phosphoglucosamine mutase (PNGM),
           phosphoacetylglucosamine mutase (PAGM), the bacterial
           phosphomannomutase ManB, the bacterial
           phosphoglucosamine mutase GlmM, and the bifunctional
           phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
           these enzymes has four domains with a centrally located
           active site formed by four loops, one from each domain.
           All four domains are included in this alignment model..
          Length = 548

 Score = 28.0 bits (63), Expect = 5.4
 Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 1/38 (2%)

Query: 135 DRKQIIGKKFFSSPA-SWRKIAHTISDDIYQSITGEKG 171
           DR  I+GK FF +P+ S   IA       Y    G KG
Sbjct: 282 DRNMILGKGFFVTPSDSVAVIAANAKLIPYFYKGGLKG 319


  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
   0.318    0.134    0.385 

Gapped
Lambda     K      H
   0.267   0.0793    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,304,255
Number of extensions: 278515
Number of successful extensions: 672
Number of sequences better than 10.0: 1
Number of HSP's gapped: 651
Number of HSP's successfully gapped: 38
Length of query: 447
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 350
Effective length of database: 4,167,664
Effective search space: 1458682400
Effective search space used: 1458682400
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: 59 (26.4 bits)