RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780687|ref|YP_003065100.1| flagellar C-ring protein
[Candidatus Liberibacter asiaticus str. psy62]
         (318 letters)



>gnl|CDD|32053 COG1868, FliM, Flagellar motor switch protein [Cell motility and
           secretion].
          Length = 332

 Score =  135 bits (342), Expect = 1e-32
 Identities = 61/324 (18%), Positives = 128/324 (39%), Gaps = 16/324 (4%)

Query: 4   QSIHKNTSPLHPI---LLARLTGKLGDKKTIEKISS--SLGYLYKKFLPKIFKEKMDLDV 58
             + +    L       +     K  D+ + E++ +   +   + + L       +   V
Sbjct: 15  SGVSEGVEELKEEDERKVKPYDFKRPDRFSKEQLRTLEIIHERFARLLTTSLSNLLRRSV 74

Query: 59  DISYTSCQSGKFSHIIHSFKENFVFSQASLSSWSSNFFIGCSNNLVITLLENLLGASHET 118
           D+   S     +   I S     + +  S+        +    +LV  +++ L G     
Sbjct: 75  DVEVGSVDQMTYEEFIRSLPNPTILNLFSMKPLKGTALLEFDPSLVFIMVDRLFGGDGRF 134

Query: 119 IPQLYNRSLSTVEKKLAKRTIAQISAVLNQCISTTQESSPNLEDFYDIDYLKKNTNRLSN 178
             +   R L+ +E+++  + + +I   L +  +   E  P +          +      N
Sbjct: 135 PAKPEGRELTDIEQRVITKLLERILEALKEAWNAVIELEPEIVRSETNPQFAQIV--SPN 192

Query: 179 EFVTTINMNMTIENVASSFVLIIPQETLLKTTLISLSSQNKSENQSED--LIDPFARKTY 236
           E V  I + + I N++  F + IP   L       LSS+ +   + +D        ++  
Sbjct: 193 EIVVLITLEVEIGNLSGMFNICIPYSMLEP-IREKLSSRMQENTREKDPEWRKELRQQVQ 251

Query: 237 QLNVNIDTRINLKKTTLKDVVTLKIGQVIPFLHREKTC---AILSANGKEIYSCELGRVG 293
           ++ V ++ R+     TL++++ L++G VIP    EK       +S  GK  + C+ G+ G
Sbjct: 252 RVEVELEARLGEISLTLREILRLEVGDVIPL---EKPADDRVTVSVGGKPKFLCQYGKSG 308

Query: 294 KNYTIRITDRINFDQKSLKNFLHK 317
             Y ++I + IN +++SL   L K
Sbjct: 309 GQYAVKILELINSEEESLDELLPK 332


>gnl|CDD|144589 pfam01052, SpoA, Surface presentation of antigens (SPOA).  This
           family includes the C-terminal region of flagellar motor
           switch proteins FliN and FliM. It is associated with
           family FliM, pfam02154.
          Length = 77

 Score = 53.3 bits (129), Expect = 9e-08
 Identities = 21/74 (28%), Positives = 38/74 (51%)

Query: 231 FARKTYQLNVNIDTRINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKEIYSCELG 290
            A +   + V ++  +   + TL +++ LK+G VIP     +    L  NG+ I+  ELG
Sbjct: 1   LAEELSDVPVELEAVLGRTELTLGELLNLKVGDVIPLDKPAEDPVELYVNGRPIFRGELG 60

Query: 291 RVGKNYTIRITDRI 304
            +G    +RIT+ +
Sbjct: 61  VIGGKLAVRITELL 74


>gnl|CDD|32070 COG1886, FliN, Flagellar motor switch/type III secretory pathway
           protein [Cell motility and secretion / Intracellular
           trafficking and secretion].
          Length = 136

 Score = 42.7 bits (100), Expect = 1e-04
 Identities = 27/115 (23%), Positives = 47/115 (40%), Gaps = 9/115 (7%)

Query: 189 TIENVASSFVLIIPQETLLKTTLISLSSQNKSENQSEDLIDPFARKTYQLNVNIDTRINL 248
             E  A S +    +E       ++ S+  +S N+S DL+         + V +   +  
Sbjct: 29  GSEATADSLLYKSVKEVAFAEVELTESTVLESLNESIDLLL-------DIPVRLSVELGR 81

Query: 249 KKTTLKDVVTLKIGQVIPF-LHREKTCAILSANGKEIYSCELGRVGKNYTIRITD 302
            K  L +++ L  G VI       +   IL  NG+ I   E+  V   + +RIT+
Sbjct: 82  TKMPLGELLALGKGSVIELDKLAGEPVDIL-VNGRLIGRGEVVVVDDKFGVRITE 135


>gnl|CDD|39724 KOG4524, KOG4524, KOG4524, Uncharacterized conserved protein
           [Function unknown].
          Length = 1014

 Score = 32.7 bits (74), Expect = 0.13
 Identities = 27/128 (21%), Positives = 52/128 (40%), Gaps = 7/128 (5%)

Query: 70  FSHIIHSFKENFVFSQASLSSWSSNFFIGCSNNLV---ITLLENLLGASHETIPQLYNRS 126
              II   K N    + +L+ + S     C N+L      LLE+L+   ++  P+L +  
Sbjct: 280 LKAIIPLRKHNNESVREALADFVSILLTRCENSLNNCEKHLLESLVHLENDENPKLPSHC 339

Query: 127 LSTVEKKLAKRTIAQISAVLNQCI---STTQESSPNLEDFYDIDYLK-KNTNRLSNEFVT 182
           +  +E    +        +L +     S    S  +LE F ++D +  +  N+L      
Sbjct: 340 VKLLEVLNEQLHNKLSDIILFENAHRLSRLSFSITDLEKFAELDTMILEVVNKLFELLNE 399

Query: 183 TINMNMTI 190
           +I++   I
Sbjct: 400 SIHLPSLI 407


>gnl|CDD|37571 KOG2360, KOG2360, KOG2360, Proliferation-associated nucleolar
           protein (NOL1) [Cell cycle control, cell division,
           chromosome partitioning].
          Length = 413

 Score = 27.6 bits (61), Expect = 4.7
 Identities = 11/41 (26%), Positives = 14/41 (34%), Gaps = 8/41 (19%)

Query: 245 RINLKKTTLKDVVTLKIGQVIPFLHREKTCAILSANGKEIY 285
           RIN  K T          + + +L  EK   I      E Y
Sbjct: 135 RINTLKGTT--------DEALDYLDYEKWKMITELKPDEFY 167


>gnl|CDD|38832 KOG3626, KOG3626, KOG3626, Organic anion transporter [Secondary
           metabolites biosynthesis, transport and catabolism].
          Length = 735

 Score = 27.2 bits (60), Expect = 5.9
 Identities = 20/94 (21%), Positives = 32/94 (34%), Gaps = 9/94 (9%)

Query: 80  NFVFSQASLSSWSSNFFIGCSNN----LVITLLENLLGASHETIPQLYNRSLSTVEKKL- 134
             V S  SL  +S  FFIGC ++    +  +   +    SHE      N   S    +  
Sbjct: 467 VIVCSVLSLLFYSLLFFIGCESSPVAGVTNSYEGSPAFTSHENPFSSCNSDCSCDTSEYE 526

Query: 135 ---AKRTIAQISAVLNQCISTTQESSPNLEDFYD 165
               +  I   S     C  ++  S  N   + +
Sbjct: 527 PVCGENGITYFSPCHAGCTESSGTSDGNT-IYTN 559


>gnl|CDD|35497 KOG0276, KOG0276, KOG0276, Vesicle coat complex COPI, beta' subunit
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 794

 Score = 27.2 bits (60), Expect = 6.0
 Identities = 15/57 (26%), Positives = 26/57 (45%)

Query: 257 VTLKIGQVIPFLHREKTCAILSANGKEIYSCELGRVGKNYTIRITDRINFDQKSLKN 313
           VT+K+G+  P +  +    I+ A   EI +  L  VG    +   +R+    K L +
Sbjct: 293 VTVKLGREEPAVSMDSNGKIIWAVHSEIQAVNLKSVGAQKEVTDGERLPLSVKELGS 349


>gnl|CDD|153057 cd00037, CLECT, C-type lectin (CTL)/C-type lectin-like (CTLD)
           domain.  CLECT: C-type lectin (CTL)/C-type lectin-like
           (CTLD) domain; protein domains homologous to the
           carbohydrate-recognition domains (CRDs) of the C-type
           lectins.  This group is chiefly comprised of eukaryotic
           CTLDs, but contains some, as yet functionally
           uncharacterized, bacterial CTLDs.  Many CTLDs are
           calcium-dependent carbohydrate binding modules; other
           CTLDs bind protein ligands, lipids, and inorganic
           surfaces, including CaCO3 and ice.  Animal C-type
           lectins are involved in such functions as extracellular
           matrix organization, endocytosis, complement activation,
           pathogen recognition, and cell-cell interactions. For
           example: mannose-binding lectin and lung surfactant
           proteins A and D bind carbohydrates on surfaces (e.g.
           pathogens, allergens, necrotic, and apoptotic cells) and
           mediate functions associated with killing and
           phagocytosis;  P (platlet)-, E (endothelial)-, and L
           (leukocyte)- selectins (sels) mediate the initial
           attachment, tethering, and rolling of lymphocytes on
           inflamed vascular walls enabling subsequent lymphocyte
           adhesion and transmigration.  CTLDs may bind a variety
           of carbohydrate ligands including mannose,
           N-acetylglucosamine, galactose, N-acetylgalactosamine,
           and fucose.  Several CTLDs bind to protein ligands, and
           only some of these binding interactions are
           Ca2+-dependent; including the CTLDs of Coagulation
           Factors IX/X (IX/X) and Von Willebrand Factor (VWF)
           binding proteins, and natural killer cell receptors.
           C-type lectins, such as lithostathine, and some type II
           antifreeze glycoproteins function in a Ca2+-independent
           manner to bind inorganic surfaces.  Many proteins in
           this group contain a single CTLD; these CTLDs associate
           with each other through several different surfaces to
           form dimers, trimers, or tetramers, from which
           ligand-binding sites project in different orientations.
           Various vertebrate type 1 transmembrane proteins
           including macrophage mannose receptor, endo180,
           phospholipase A2 receptor, and dendritic and epithelial
           cell receptor (DEC205) have extracellular domains
           containing 8 or more CTLDs; these CTLDs remain in the
           parent model.  In some members (IX/X and VWF binding
           proteins), a loop extends to the adjoining domain to
           form a loop-swapped dimer.  A similar conformation is
           seen in the macrophage mannose receptor CRD4's putative
           non-sugar bound form of the domain in the acid
           environment of the endosome.  Lineage specific
           expansions of CTLDs have occurred in several animal
           lineages including Drosophila melanogaster and
           Caenorhabditis elegans; these CTLDs also remain in the
           parent model.
          Length = 116

 Score = 26.8 bits (59), Expect = 8.2
 Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 7/58 (12%)

Query: 48  KIFKEKMDLDVDISYTSCQSGKFSH--IIHSFKEN-FVFSQASLSSWSSNFFIGCSNN 102
           K   EK+  +   +   C+S    H   IHS +EN F+ S     S SS+ +IG ++ 
Sbjct: 4   KFSTEKLTWEE--AQEYCRS-LGGHLASIHSEEENDFLASLLK-KSSSSDVWIGLNDL 57


  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    0.132    0.365 

Gapped
Lambda     K      H
   0.267   0.0724    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,508,684
Number of extensions: 174436
Number of successful extensions: 417
Number of sequences better than 10.0: 1
Number of HSP's gapped: 413
Number of HSP's successfully gapped: 23
Length of query: 318
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 224
Effective length of database: 4,232,491
Effective search space: 948077984
Effective search space used: 948077984
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: 57 (25.7 bits)