RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781007|ref|YP_003065420.1| hypothetical protein
CLIBASIA_04540 [Candidatus Liberibacter asiaticus str. psy62]
         (411 letters)



>gnl|CDD|177239 MTH00191, CYTB, cytochrome b; Provisional.
          Length = 365

 Score = 29.5 bits (67), Expect = 1.8
 Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 10/46 (21%)

Query: 210 TLVKNFLSQIPYKNFCMAPYHYSSILYWAVGTLTYSVDNKTTTREY 255
           T++ N LS IPY            ++ W  G   +SVDN T TR +
Sbjct: 141 TVITNLLSAIPYIG--------DDLVQWLWGG--FSVDNATLTRFF 176


>gnl|CDD|39700 KOG4500, KOG4500, KOG4500, Rho/Rac GTPase guanine nucleotide
           exchange factor smgGDS/Vimar [Signal transduction
           mechanisms].
          Length = 604

 Score = 28.5 bits (63), Expect = 3.4
 Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 5/53 (9%)

Query: 283 FGDGQVLTNTNHCFPHGASQNKYMLMLAIGNQLSRSS-----VEKEKIEKVLQ 330
             D Q L      F    S    M  LAIGN   R       V+K+ + K++ 
Sbjct: 311 HADPQFLDFLESWFRSDDSNLITMGSLAIGNFARRDDICIQLVQKDFLNKLIS 363


>gnl|CDD|35313 KOG0090, KOG0090, KOG0090, Signal recognition particle receptor,
           beta subunit (small G protein superfamily)
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 238

 Score = 28.4 bits (63), Expect = 3.8
 Identities = 23/93 (24%), Positives = 36/93 (38%), Gaps = 11/93 (11%)

Query: 31  SSFVAIVDVVVDQVTVMQKTAWLQEVLDHVIYRTSPK----------NLYDLREAGRDNF 80
           +     +  VVD  T ++    + E L  ++  +  K          N  DL  A     
Sbjct: 106 NYSAKAIVFVVDSATFLKNVRDVAEFLYDILLDSRVKKNKPPVLIACNKQDLFTAKTAEK 165

Query: 81  IRHQIEKALNTYN-SRDLSNTGSIESIVKDAVI 112
           IR Q+EK ++    SR    + S E I KD  +
Sbjct: 166 IRQQLEKEIHKLRESRSALRSISDEDIAKDFTL 198


>gnl|CDD|133316 cd04116, Rab9, Rab9 subfamily.  Rab9 is found in late endosomes,
           together with mannose 6-phosphate receptors (MPRs) and
           the tail-interacting protein of 47 kD (TIP47).  Rab9 is
           a key mediator of vesicular transport from late
           endosomes to the trans-Golgi network (TGN) by
           redirecting the MPRs.  Rab9 has been identified as a key
           component for the replication of several viruses,
           including HIV1, Ebola, Marburg, and measles, making it a
           potential target for inhibiting a variety of viruses.
           GTPase activating proteins (GAPs) interact with
           GTP-bound Rab and accelerate the hydrolysis of GTP to
           GDP. Guanine nucleotide exchange factors (GEFs) interact
           with GDP-bound Rabs to promote the formation of the
           GTP-bound state.  Rabs are further regulated by guanine
           nucleotide dissociation inhibitors (GDIs), which
           facilitate Rab recycling by masking C-terminal lipid
           binding and promoting cytosolic localization.  Most Rab
           GTPases contain a lipid modification site at the
           C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
           binding is essential for membrane attachment, a key
           feature of most Rab proteins.  Due to the presence of
           truncated sequences in this CD, the lipid modification
           site is not available for annotation.
          Length = 170

 Score = 27.9 bits (62), Expect = 5.1
 Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 9/66 (13%)

Query: 242 LTYSVDNKTTTREY--YKDP--YYA---TWDHFPYSFIKNVFDMTSNQFG--DGQVLTNT 292
           LT++VD+  + +    +K    YYA     + FP+  + N  D+   Q    + Q     
Sbjct: 83  LTFAVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVVLGNKNDIPERQVSTEEAQAWCRE 142

Query: 293 NHCFPH 298
           N  +P+
Sbjct: 143 NGDYPY 148


>gnl|CDD|177109 MTH00034, CYTB, cytochrome b; Validated.
          Length = 379

 Score = 27.7 bits (62), Expect = 5.2
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 18/63 (28%)

Query: 210 TLVKNFLSQIPYKNFCMAPYHYSSILYWAVGTLTYSVDNKTTTREYYKDPYYATWDHFPY 269
           T++ N +S +PY          + I+ W  G   +SVDN T TR      ++A   HF +
Sbjct: 144 TVITNLVSAVPYIG--------TDIVQWIWGG--FSVDNATLTR------FFAF--HFLF 185

Query: 270 SFI 272
            FI
Sbjct: 186 PFI 188


>gnl|CDD|35436 KOG0215, KOG0215, KOG0215, RNA polymerase III, second largest
           subunit [Transcription].
          Length = 1153

 Score = 27.6 bits (61), Expect = 7.2
 Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 16/77 (20%)

Query: 331 DCHYMHKRHRTGRDAITIFSVGFSP-------------DQDTRYTLRQCASDPSKYYEIN 377
           D  Y   R    +  + I   G  P             D++    L +C  DP  Y+ + 
Sbjct: 137 DIEYTRGRQIIAKRDVII---GRMPIMLRSSKCVLRGKDEEELARLNECPLDPGGYFIVK 193

Query: 378 SDENVMPIAKSLARNVI 394
             E V+ I + L++N I
Sbjct: 194 GTEKVILIQEQLSKNRI 210


>gnl|CDD|35549 KOG0328, KOG0328, KOG0328, Predicted ATP-dependent RNA helicase
           FAL1, involved in rRNA maturation, DEAD-box superfamily
           [Translation, ribosomal structure and biogenesis].
          Length = 400

 Score = 27.2 bits (60), Expect = 9.1
 Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 334 YMHKRHRTGRDAITIFSVGFSPDQDTRYTLRQCASDPSKYYEINSDENVMPIAKSL 389
           Y+H+  R+GR      ++ F    D R  LR    D  +YY    DE  M +A  +
Sbjct: 350 YIHRIGRSGRFGRKGVAINFVKSDDLR-ILR----DIEQYYSTQIDEMPMNVADLI 400


  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
   0.322    0.134    0.404 

Gapped
Lambda     K      H
   0.267   0.0740    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,974,823
Number of extensions: 258639
Number of successful extensions: 570
Number of sequences better than 10.0: 1
Number of HSP's gapped: 564
Number of HSP's successfully gapped: 16
Length of query: 411
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 315
Effective length of database: 4,189,273
Effective search space: 1319620995
Effective search space used: 1319620995
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 (21.9 bits)
S2: 59 (26.5 bits)