RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780721|ref|YP_003065134.1| pilus component protein
[Candidatus Liberibacter asiaticus str. psy62]
         (329 letters)



>gnl|CDD|32247 COG2064, TadC, Flp pilus assembly protein TadC [Cell motility and
           secretion / Intracellular trafficking and secretion].
          Length = 320

 Score =  115 bits (288), Expect = 2e-26
 Identities = 98/322 (30%), Positives = 148/322 (45%), Gaps = 5/322 (1%)

Query: 8   LFDATELAVAITTAVSIFSLIYAVVIPSLGSGELEKRMKSVAVEREILRKQQITSLQKDS 67
           L    EL +    A  +F+L   VV+  L   EL   +K V  E   +    +  L   S
Sbjct: 1   LLMRAELYLTFLVARPLFALAILVVMAVLKRKELLLLLKGVDREIPRIILLSLIRLLIGS 60

Query: 68  ASSRLRTRDSKSLRNFVKKLNLKAILVDENIVNKLRAAGFRSEYSLNILLVVRLVVPII- 126
            S R        LR  +  L L     D     KL  A +R E +L + L   L+   + 
Sbjct: 61  VSIRELLAFL--LRKIISGLLLFFGGEDSKPRFKLVEALYRLELALPLFLFALLLALFLG 118

Query: 127 FLILGIIWIFGYDKLLEYPFQLRVGAVILIGYVGFCAPSVWISNLVQKRQSSIKRAWPDA 186
            L+   I +      +  P    +   +LI  +G   P +  S  ++KR   I R  PD 
Sbjct: 119 VLLSLPILLLVLGSFIILPLSDFLAIALLISLLGLPLPFILFSLALKKRLKEIARELPDF 178

Query: 187 LDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNRT 246
           L L+ +C+E+G+S+  AL+RVA+++ GQ   L+EE+  T AELS   + + A      R 
Sbjct: 179 LRLMAVCLEAGLSLADALKRVADELYGQ-RILAEELARTTAELSLGLSIEEALIRLAVRL 237

Query: 247 QMDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSE-RLMEAEKKAASLGPKLTVPMIIF 305
             D V+     L Q+   G S+ D+LRVL  E   E RL   E +A  +G  + +P+I+ 
Sbjct: 238 GSDEVKRVVSLLTQALESGGSLADALRVLSMELSRETRLKLGEIRAGKIGVGILLPLILV 297

Query: 306 FLPVLILVIIGPAILSIIDTMK 327
            +PVL+ V+I PAIL I  +  
Sbjct: 298 IIPVLLFVVILPAILGIASSGG 319


>gnl|CDD|144175 pfam00482, GSPII_F, Bacterial type II secretion system protein F
           domain.  The original family covered both the regions
           found by the current model. The splitting of the family
           has allowed the related FlaJ_arch (archaeal FlaJ family)
           to be merged with it. Proteins with this domain in form
           a platform for the type II secretion machinery, as well
           as the type IV pili and the archaeal flagellae. This
           domain seems to show some similarity to pfam00664, but
           this may just be due to similarities in the TM helices
           (personal obs: C Yeats).
          Length = 125

 Score = 62.7 bits (153), Expect = 1e-10
 Identities = 28/131 (21%), Positives = 54/131 (41%), Gaps = 6/131 (4%)

Query: 186 ALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAFENFYNR 245
            L  L   + +G+ + +AL  +AE+    + PL EE+      L    +   A      R
Sbjct: 1   FLRQLATLLRAGLPLLEALEILAEEAE--NGPLREELKRIRERLREGGSLSEALA----R 54

Query: 246 TQMDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLTVPMIIF 305
           T +        ALI +   G ++ + L  L       R +  +  AA L P + + + + 
Sbjct: 55  TPLSEFPPLLVALIAAGESGGNLAEVLERLADYLEERRELRRKILAALLYPLILLVVALL 114

Query: 306 FLPVLILVIIG 316
            L +L+ +++ 
Sbjct: 115 VLLILLAILLP 125


>gnl|CDD|34572 COG4965, TadB, Flp pilus assembly protein TadB [Intracellular
           trafficking and secretion].
          Length = 309

 Score = 54.5 bits (131), Expect = 4e-08
 Identities = 41/196 (20%), Positives = 77/196 (39%), Gaps = 8/196 (4%)

Query: 120 RLVVPIIFLILGIIWIFGYDKLLEYPFQLRVGAVILIGYVGFCAPSVWISNLVQKRQSSI 179
             +  +I L  G         +      L V  V LIG        +   +   +R    
Sbjct: 79  VSLARLILLSAGAGLAVAL--VAWLGLSLLVALVALIGAALLPRLVLR--SRRARRLKRF 134

Query: 180 KRAWPDALDLLLICVESGISIDQALRRVAEDIGGQSVPLSEEMLLTIAELSFLPNRQVAF 239
            +  P+ALDL++  + +G  +  ALR  A++      PL  E  L         +   A 
Sbjct: 135 GQQLPEALDLIVRALRAGAPLPDALRLAAKETPE---PLGTEFTLITDRQQLGIDLPAAL 191

Query: 240 ENFYNRTQMDCVRNATQALIQSDRYGTSIGDSLRVLVSETRSERLMEAEKKAASLGPKLT 299
              Y R  ++ +      +    R+G ++ + L  L    R  + M+A+ +A S   +++
Sbjct: 192 LRMYERYPLEELYFLAIVISIQSRHGGNLSELLDNLSRVIRERKKMKAKVRALSAEARMS 251

Query: 300 VPMIIFFLPVLILVII 315
              I+  LP+L+ ++I
Sbjct: 252 A-WILGALPLLVGLLI 266


>gnl|CDD|31669 COG1480, COG1480, Predicted membrane-associated HD superfamily
           hydrolase [General function prediction only].
          Length = 700

 Score = 31.1 bits (70), Expect = 0.47
 Identities = 23/115 (20%), Positives = 45/115 (39%), Gaps = 9/115 (7%)

Query: 50  VEREILRKQQITSLQKDSASSRLRTRDSKSLRNFVKKLNLKAIL-----VDENIVNKLRA 104
              EIL      +   D   +    +++ S    VK    + I+     + +     L  
Sbjct: 205 AATEILNSALKPNYVYDEEQTENLRQEALSKVEPVKISKGQIIVKEGEIITDEDYVILDL 264

Query: 105 AGFRSEYSLNILLVVRLVVPIIFLILGIIWIFGYDKLLEYPFQLRVGAVILIGYV 159
            G     S+NIL ++ L   +I +I  I+    Y++  + P +LR   ++L   +
Sbjct: 265 LGL-LSLSVNILPLLGL---LILVIFLILLFALYERRTKSPLKLRNSLLLLYLSL 315


>gnl|CDD|39872 KOG4673, KOG4673, KOG4673, Transcription factor TMF, TATA element
           modulatory factor [Transcription].
          Length = 961

 Score = 29.8 bits (66), Expect = 0.98
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 8/71 (11%)

Query: 40  ELEKRMKSVAVEREILRKQQITSLQKDSASSRLRTRDSKSLRNFVKKLNL------KAIL 93
            LEK+++++  ER+ LR++Q     K   ++ L   +       + +L        K  L
Sbjct: 413 TLEKKVQALTKERDALRREQ--KSLKKELAAALLKDELAEKDEIINQLMAEGEKLSKKQL 470

Query: 94  VDENIVNKLRA 104
               I+ KLRA
Sbjct: 471 AQSAIIKKLRA 481


>gnl|CDD|143474 cd07322, PriL_PriS_Eukaryotic, Eukaryotic core primase: Large
           subunit, PriL.  Primases synthesize the RNA primers
           required for DNA replication. Primases are grouped into
           two classes, bacteria/bacteriophage and
           archaeal/eukaryotic. The proteins in the two classes
           differ in structure and the replication apparatus
           components. Archaeal/eukaryotic core primase is a
           heterodimeric enzyme consisting of a small catalytic
           subunit (PriS) and a large subunit (PriL). In eukaryotic
           organisms, a heterotetrameric enzyme formed by DNA
           polymerase alpha, the B subunit and two primase subunits
           has primase activity. Although the catalytic activity
           resides within PriS, the PriL subunit is essential for
           primase function as disruption of the PriL gene in yeast
           is lethal. PriL is composed of two structural domains.
           Several functions have been proposed for PriL such as
           stabilization of the PriS, involvement in synthesis
           initiation, improvement of primase processivity,
           determination of product size and transfer of the
           products to DNA polymerase alpha.
          Length = 390

 Score = 27.6 bits (62), Expect = 5.5
 Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 13/73 (17%)

Query: 42  EKRMKSVAVEREILRKQQITSLQKDSASSRLRTRDSKSLRNFVKKLNLKAILVDENIVNK 101
           E R   V  E E+ R              RL     + L+ F+K   L    V +    +
Sbjct: 55  ELRRWFVRQETELFRY-------------RLELLSLEGLKQFLKSNGLDYQPVSDEEKEE 101

Query: 102 LRAAGFRSEYSLN 114
           LR    +S  SL 
Sbjct: 102 LREELLKSASSLK 114


>gnl|CDD|38163 KOG2952, KOG2952, KOG2952, Cell cycle control protein [Cell cycle
           control, cell division, chromosome partitioning,
           Transcription, Signal transduction mechanisms].
          Length = 351

 Score = 27.2 bits (60), Expect = 5.7
 Identities = 15/89 (16%), Positives = 36/89 (40%), Gaps = 11/89 (12%)

Query: 103 RAAGFRSEYSLNILLVVRLVVPIIFLILGIIWIFGYDKLLEYPFQLRVGAVILIGYVGFC 162
           R   ++   +   +L +  ++ ++FL +G+  +F   K++E          I I Y   C
Sbjct: 32  RLPAWQPILTPRTVLPLFFIIGVVFLPIGVGLLFASSKVIE----------ITIRYTD-C 80

Query: 163 APSVWISNLVQKRQSSIKRAWPDALDLLL 191
            P+ + +N  +  Q    +     +   +
Sbjct: 81  IPTGFRTNPSEYIQGHFDQTKSCTITFTV 109


>gnl|CDD|37930 KOG2719, KOG2719, KOG2719, Metalloprotease [General function
           prediction only].
          Length = 428

 Score = 27.1 bits (60), Expect = 6.0
 Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 99  VNKLRAAGFRSEYSLNILLVVRLVVPIIFLILGIIWIFGYDKLLE-YPFQLRVGAVILIG 157
            NK   + F  +   ++L+ V L +PI+  I+ I+  FG    +  + F   +  ++L  
Sbjct: 140 FNKQTLSLFIIDGLKSLLVGVVLTIPIVAAIVMILKKFGPYFFIYLWLFYFVLSLLLLTI 199

Query: 158 YVGFCAPSV 166
           Y GF AP  
Sbjct: 200 YPGFIAPLF 208


>gnl|CDD|31175 COG0833, LysP, Amino acid transporters [Amino acid transport and
           metabolism].
          Length = 541

 Score = 26.7 bits (59), Expect = 9.8
 Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 4/41 (9%)

Query: 98  IVNKLRAAGF-RSEYSLNILLVVRLVVPIIFLILGIIWIFG 137
           ++N     GF  +E+  + + V+ +   I F+ILGII I G
Sbjct: 173 LLNLFGVKGFGETEFWFSSIKVLTI---IGFIILGIIIICG 210


  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
   0.325    0.139    0.390 

Gapped
Lambda     K      H
   0.267   0.0753    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,791,209
Number of extensions: 200999
Number of successful extensions: 1044
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1042
Number of HSP's successfully gapped: 32
Length of query: 329
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 235
Effective length of database: 4,232,491
Effective search space: 994635385
Effective search space used: 994635385
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.1 bits)