RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780529|ref|YP_003064942.1| flagellar motor protein MotB
[Candidatus Liberibacter asiaticus str. psy62]
         (343 letters)



>gnl|CDD|31551 COG1360, MotB, Flagellar motor protein [Cell motility and
           secretion].
          Length = 244

 Score = 95.8 bits (238), Expect = 1e-20
 Identities = 50/168 (29%), Positives = 80/168 (47%), Gaps = 11/168 (6%)

Query: 179 SKEKILAMKRKKRLQDLAKKISSTLSGLVADNIVKG-VLFETTRTGILISIIDQRNTPMF 237
             E I   +  ++L DLAK++ S       D  ++  +  +    G++ISI D     MF
Sbjct: 84  VGEAIEKKELSEKLGDLAKELES----KPKDIELEHQLGVDDVEEGLVISISDSL---MF 136

Query: 238 DKSSSIPLPETIVVLQKIGEVLA-HSTEVISIRGHTDASPFRNIARDNWRLSLDRAYSAY 296
              S++  PE   +L KI ++LA      I I GHTD  P +     NW LS  RA S  
Sbjct: 137 ASGSAVVQPEFRDLLLKIAKLLADIPNGNIRIEGHTDNVPIKGSFYSNWELSAARAQSVV 196

Query: 297 QVLMKSGVSEDRISKISGFAHHRLKI--ASDPMNSANRRIDILVEDRQ 342
           +VL+  G+ E +   + G+A  R      +    + NRR++IL+  ++
Sbjct: 197 RVLINGGLVEAKRLSVVGYADTRPLADNDTAEGRAKNRRVEILILTKK 244



 Score = 61.6 bits (149), Expect = 3e-10
 Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 27 PNNLGSWKIVYADFMTVLMAFFLVMWIINATDDDTKKAIEQYFNP-FGKNLMTASKGIFD 85
           +  G+WKI YADFMT+L+AFF+V+W +++   +  + I  YF   F     +AS+G   
Sbjct: 10 QHGGGAWKIAYADFMTLLLAFFIVLWAMSSISPEKFQQIAAYFRIAFSGAPGSASEGGKS 69

Query: 86 EQNPPERSSQNKID 99
           Q   E+    +++
Sbjct: 70 MQQVKEKELAEELN 83


>gnl|CDD|143586 cd07185, OmpA_C-like, Peptidoglycan binding domains similar to the
           C-terminal domain of outer-membrane protein OmpA.
           OmpA-like domains (named after the C-terminal domain of
           Escherichia coli OmpA protein) have been shown to
           non-covalently associate with peptidoglycan, a network
           of glycan chains composed of disaccharides, which are
           crosslinked via short peptide bridges. Well-studied
           members of this family include the Escherichia coli
           outer membrane protein OmpA, the Escherichia coli
           lipoprotein PAL, Neisseria meningitdis RmpM, which
           interact with the outer membrane, as well as the
           Escherichia coli motor protein MotB, and the Vibrio
           flagellar motor proteins PomB and MotY, which interact
           with the inner membrane.
          Length = 106

 Score = 73.0 bits (180), Expect = 1e-13
 Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 5/104 (4%)

Query: 237 FDKSSSIPLPETIVVLQKIGEVL-AHSTEVISIRGHTDASPFRNIARDNWRLSLDRAYSA 295
           FD  S+   PE   +L K+ EVL  +    I I GHTD+   R     N  LS  RA + 
Sbjct: 6   FDFGSAELTPEAKPLLDKLAEVLKKNPDAKIRIEGHTDS---RGSDAYNQELSERRAEAV 62

Query: 296 YQVLMKSGVSEDRISKIS-GFAHHRLKIASDPMNSANRRIDILV 338
              L+  GV   RI+ +  G +       ++   + NRR++I++
Sbjct: 63  ADYLVSKGVDASRITAVGYGESRPIASNDTEEGRAKNRRVEIVI 106


>gnl|CDD|144333 pfam00691, OmpA, OmpA family.  The Pfam entry also includes MotB
           and related proteins which are not included in the
           Prosite family.
          Length = 97

 Score = 57.1 bits (138), Expect = 6e-09
 Identities = 29/100 (29%), Positives = 38/100 (38%), Gaps = 5/100 (5%)

Query: 236 MFDKSSSIPLPETIVVLQKIGEVLAHS--TEVISIRGHTDASPFRNIARDNWRLSLDRAY 293
           +FD  S+    E    L ++ EVL        I I GHTD+      A+ NW LS  RA 
Sbjct: 1   LFDPGSAELTAEARETLDRLAEVLKAPELKIAIKIEGHTDSRG---SAKYNWELSARRAQ 57

Query: 294 SAYQVLMKSGVSEDRISKISGFAHHRLKIASDPMNSANRR 333
           +    L+  G+   RIS         L         A  R
Sbjct: 58  AVANYLVNHGIPPSRISVEGYGESQPLASNDSDEGRAKNR 97


>gnl|CDD|32711 COG2885, OmpA, Outer membrane protein and related
           peptidoglycan-associated (lipo)proteins [Cell envelope
           biogenesis, outer membrane].
          Length = 190

 Score = 52.1 bits (124), Expect = 2e-07
 Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 9/116 (7%)

Query: 227 SIIDQRNTPMFDKSSSIPLPETIVVLQKIGEVL-AHSTEVISIRGHTDA--SPFRNIARD 283
            I++  N  +FD  SS+  P+    L ++ + L  +    I + GHTD+  S   N A  
Sbjct: 77  IILNLPNDVLFDFDSSVLKPKAQATLDELAKYLKKNPITRILVEGHTDSTGSDEYNQA-- 134

Query: 284 NWRLSLDRAYSAYQVLMKSGVSEDRISKIS-GFAHHRLKIASDPMNSANRRIDILV 338
              LS  RA +    L+  GV  DRIS +  G        A++   + NRR++I +
Sbjct: 135 ---LSERRAEAVADYLVSQGVVADRISTVGYGEEKPIASNATEEGRAKNRRVEIKI 187


>gnl|CDD|36433 KOG1219, KOG1219, KOG1219, Uncharacterized conserved protein,
            contains laminin, cadherin and EGF domains [Signal
            transduction mechanisms].
          Length = 4289

 Score = 31.5 bits (71), Expect = 0.29
 Identities = 45/210 (21%), Positives = 70/210 (33%), Gaps = 44/210 (20%)

Query: 74   KNLMTASKGIFDEQNPPERSSQNKIDLSIDEHITKNSVDLKIGSTNQKKQYQRLENNIFY 133
            KN       ++D  +   R + N     + E     +V L++ + ++     R EN I Y
Sbjct: 1448 KNFAMTLINVYDSNDHSPRFTTNNYLALVSESHAVGTVLLQVTAEDK----DRGENAIVY 1503

Query: 134  LSNSQQSEHCKNSLTRDSEKGKDLCKSTDLEKSINKEENYFLPPLSKEKILAMKRKKRLQ 193
             S                  G                E + +     E ILA    KRL 
Sbjct: 1504 YS---------------IGSGN--------------IELFKIDADLGEIILA----KRL- 1529

Query: 194  DLAKKISSTLSGLVADNIVKGVLFETTRTGILISIIDQRNTPMFDKSS-SIPLPETIVVL 252
            D        L+    D      + + + T  +  I D    P FD+S   + LPE+    
Sbjct: 1530 DELNHAERNLNVKAIDAGSPKGIDKASVT--IEVIEDDLILPKFDQSEYFVELPESFNSG 1587

Query: 253  QKIGEVLAHSTEVISIR---GHTDASPFRN 279
              IG+V A S   ++     G+T    F N
Sbjct: 1588 SPIGKVPADSDSDVTYELIDGNTYVRFFEN 1617


>gnl|CDD|132855 cd07216, Pat17_PNPLA8_PNPLA9_like3, Patatin-like phospholipase.
           Patatin is a storage protein of the potato tuber that
           shows Phospholipase A2 activity (PLA2; EC 3.1.1.4).
           Patatin catalyzes the nonspecific hydrolysis of
           phospholipids, glycolipids, sulfolipids, and mono- and
           diacylglycerols, thereby showing lipid acyl hydrolase
           activity. The active site includes an oxyanion hole with
           a conserved GGxR motif; it is found in almost all the
           members of this family. The catalytic dyad is formed by
           a serine and an aspartate. Patatin belongs to the
           alpha-beta hydrolase family which is identified by a
           characteristic nucleophile elbow with a consensus
           sequence of Sm-X-Nu-Sm (Sm = small residue, X = any
           residue and Nu = nucleophile). Members of this family
           have been found also in vertebrates. This family
           includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9
           (iPLA2-beta) like phospholipases from human as well as
           the Pat17 isozyme from Solanum cardiophyllum.
          Length = 309

 Score = 27.3 bits (61), Expect = 7.1
 Identities = 13/49 (26%), Positives = 20/49 (40%)

Query: 286 RLSLDRAYSAYQVLMKSGVSEDRISKISGFAHHRLKIASDPMNSANRRI 334
           R+++D    AY  L K   S  R+  I G      +  S  +  A + I
Sbjct: 63  RMTVDECIDAYTRLAKKIFSRKRLRLIIGDLRTGARFDSKKLAEAIKVI 111


>gnl|CDD|36277 KOG1059, KOG1059, KOG1059, Vesicle coat complex AP-3, delta subunit
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 877

 Score = 26.8 bits (59), Expect = 8.1
 Identities = 19/88 (21%), Positives = 31/88 (35%), Gaps = 3/88 (3%)

Query: 125 QRLENNIFYLSNSQQSEHCKNSLTRDSEKGKDLCKSTDLEKSIN-KEENYFLPPLSKEKI 183
           Q   NN +YL +S +++     LT    +  +      L  S            L + K 
Sbjct: 686 QEQMNNPYYLKSSPEAQ--TKLLTLSEYENVNKIPEIQLPLSDPSFNPLSLSQTLIERKK 743

Query: 184 LAMKRKKRLQDLAKKISSTLSGLVADNI 211
              K+KK++Q    K     +    DN 
Sbjct: 744 KKGKKKKKVQKKDDKKVIKKAPKRKDNF 771


>gnl|CDD|146916 pfam04515, Choline_transpo, Plasma-membrane choline transporter. 
          This family represents a high-affinity plasma-membrane
          choline transporter in C.elegans which is thought to be
          rate-limiting for ACh synthesis in colinergic nerve
          terminals.
          Length = 327

 Score = 26.8 bits (60), Expect = 8.4
 Identities = 8/38 (21%), Positives = 13/38 (34%), Gaps = 2/38 (5%)

Query: 20 KVAIDDTPNNLGSWKIVYADFMTVLMAFFLVMWIINAT 57
          K A      N      +      + +A F  +WI+ A 
Sbjct: 32 KTASKAVSKNPSL--FLVPIITFLALAAFWALWIVVAV 67


>gnl|CDD|109724 pfam00680, RdRP_1, RNA dependent RNA polymerase. 
          Length = 479

 Score = 26.9 bits (60), Expect = 9.7
 Identities = 10/39 (25%), Positives = 20/39 (51%)

Query: 148 TRDSEKGKDLCKSTDLEKSINKEENYFLPPLSKEKILAM 186
           T ++   + L + T L+++  ++E    P L KE I + 
Sbjct: 374 TSETIPIRPLEELTFLKRTFKRDEGGVRPKLDKESIFSQ 412


  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
   0.315    0.131    0.366 

Gapped
Lambda     K      H
   0.267   0.0786    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,927,692
Number of extensions: 198694
Number of successful extensions: 544
Number of sequences better than 10.0: 1
Number of HSP's gapped: 539
Number of HSP's successfully gapped: 22
Length of query: 343
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 248
Effective length of database: 4,210,882
Effective search space: 1044298736
Effective search space used: 1044298736
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 (21.6 bits)
S2: 58 (26.0 bits)