RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780380|ref|YP_003064793.1| flagellar basal body rod
protein FlgC [Candidatus Liberibacter asiaticus str. psy62]
         (134 letters)



>gnl|CDD|31746 COG1558, FlgC, Flagellar basal body rod protein [Cell motility and
           secretion].
          Length = 137

 Score =  138 bits (349), Expect = 5e-34
 Identities = 59/136 (43%), Positives = 79/136 (58%), Gaps = 7/136 (5%)

Query: 4   LIASAHIANSGLAVQSARMQIISENIANARTTGDTPGSDPYRRKTISFEEVMH------G 57
           L +  +IA S L+ QS R+ +IS NIANA +T    G  PYRRK + F   +       G
Sbjct: 3   LFSIFNIAGSALSAQSLRLNVISSNIANADSTRTPDG-GPYRRKQVVFSAELFAPTGATG 61

Query: 58  SGGVRVKKIGVDQSTFVEEFDPGHPVANASGIVKYPNVNVLVETADMRETNRLYMANLQT 117
             GV+V KI  D S F   +DPGHP A+A G VK PNVNV++E  DM   +R Y AN++ 
Sbjct: 62  GAGVKVSKIVEDPSPFKLVYDPGHPDADAKGYVKMPNVNVVIEMVDMISASRSYEANVEV 121

Query: 118 IKQSHDMMTTTLDLLR 133
           +  +  MM  TL+L +
Sbjct: 122 LNTAKSMMQKTLELGQ 137


>gnl|CDD|32000 COG1815, FlgB, Flagellar basal body protein [Cell motility and
           secretion].
          Length = 133

 Score = 48.4 bits (115), Expect = 6e-07
 Identities = 29/138 (21%), Positives = 56/138 (40%), Gaps = 15/138 (10%)

Query: 1   MDYLIASAHIANSGLAVQSARMQIISENIANARTTGDTPGSDPYRRKTISFEEVMHGSGG 60
           M     +  +    L V+S R ++I+ NIANA    DTPG   Y+ K + FE V+  +  
Sbjct: 1   MMSFDRAFGLLQKALDVRSLRQEVIANNIANA----DTPG---YKAKDVDFESVLKKALA 53

Query: 61  VRVKKIGVDQST--FVEEFD----PGHPVANASGIVKYP--NVNVLVETADMRETNRLYM 112
                + + +++   +   +        + +  G        V++  E  +  +   +Y 
Sbjct: 54  GNNTTLALAKTSTRHLGPAENIDPTDASLLDRIGDQPNDGNTVDLDREMTEFAKNQLMYQ 113

Query: 113 ANLQTIKQSHDMMTTTLD 130
           A L  +K    M+ + L 
Sbjct: 114 ALLSFLKSQIKMLNSVLK 131


>gnl|CDD|31935 COG1749, FlgE, Flagellar hook protein FlgE [Cell motility and
          secretion].
          Length = 423

 Score = 39.6 bits (92), Expect = 2e-04
 Identities = 22/81 (27%), Positives = 33/81 (40%), Gaps = 9/81 (11%)

Query: 10 IANSGLAVQSARMQIISENIANARTTGDTPGSDPYRRKTISFEEVMHGS--GGVRVKKIG 67
             SG+      + +IS NIANA TTG       ++R    F ++   S  G      +G
Sbjct: 7  NGVSGMNAHQFALDVISNNIANANTTG-------FKRSRAEFSDMFSQSLVGASTYTALG 59

Query: 68 VDQSTFVEEFDPGHPVANASG 88
          V  S+  + F  G   +  S 
Sbjct: 60 VGVSSISQIFTQGSFQSTGSN 80



 Score = 31.5 bits (71), Expect = 0.073
 Identities = 15/48 (31%), Positives = 26/48 (54%)

Query: 86  ASGIVKYPNVNVLVETADMRETNRLYMANLQTIKQSHDMMTTTLDLLR 133
           +SG ++  NV++  E  ++    R Y AN + I  S  M+ T ++L R
Sbjct: 376 SSGALEMSNVDLAKELTNLIVAQRGYQANAKVITTSDQMLQTLVNLKR 423


>gnl|CDD|34397 COG4786, FlgG, Flagellar basal body rod protein [Cell motility
          and secretion].
          Length = 265

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 7/47 (14%)

Query: 9  HIANSGLAVQSARMQIISENIANARTTGDTPGSDPYRRKTISFEEVM 55
          + A SG+  Q  ++ +IS N+AN  TTG       ++R    FE+++
Sbjct: 6  YTAASGMMAQQRKLDVISNNLANVNTTG-------FKRDRAEFEDLL 45



 Score = 32.5 bits (74), Expect = 0.035
 Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 11/79 (13%)

Query: 64  KKIGVDQSTFVEEFDPGHPVANAS---------GIVKYPNVNVLVETADMRETNRLYMAN 114
           KKIG   + + E    G  V             G ++  NVNV+ E  DM E  R Y AN
Sbjct: 189 KKIG--NNLYQETAASGPIVGVPGDNGFGAIRQGFLEASNVNVVEEMTDMIEAQRAYEAN 246

Query: 115 LQTIKQSHDMMTTTLDLLR 133
            + I+ + +M+    +LLR
Sbjct: 247 SKVIQTADEMLGKANNLLR 265


>gnl|CDD|109515 pfam00460, Flg_bb_rod, Flagella basal body rod protein. 
          Length = 31

 Score = 33.7 bits (78), Expect = 0.017
 Identities = 13/27 (48%), Positives = 16/27 (59%)

Query: 10 IANSGLAVQSARMQIISENIANARTTG 36
           A S L  Q   + +I+ NIANA TTG
Sbjct: 3  TAVSALNAQQIALDVIANNIANANTTG 29


>gnl|CDD|31448 COG1256, FlgK, Flagellar hook-associated protein [Cell motility
          and secretion].
          Length = 552

 Score = 28.8 bits (64), Expect = 0.51
 Identities = 17/64 (26%), Positives = 24/64 (37%), Gaps = 14/64 (21%)

Query: 10 IANSGLAVQSARMQIISENIANARTTGDTPGSDPYRRKTISFEEV-------MHGSGGVR 62
           A SGL    A + +   NI+NA T G       Y R+ +            ++   GV 
Sbjct: 9  TALSGLNAAQAALDVTGHNISNANTPG-------YSRQRVIQTTNIPYLGGGLNVGTGVN 61

Query: 63 VKKI 66
          V  I
Sbjct: 62 VVSI 65


>gnl|CDD|100092 cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and
           PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2
           is thought to be a phosphopentomutase that catalyzes the
           conversion of the nucleoside breakdown products,
           ribose-1-phosphate and deoxyribose-1-phosphate to the
           corresponding 5-phosphopentoses. PGM2L1 is thought to
           catalyze the 1,3-bisphosphoglycerate-dependent synthesis
           of glucose 1,6-bisphosphate and other
           aldose-bisphosphates that serve as cofactors for several
           sugar phosphomutases and possibly also as regulators of
           glycolytic enzymes. PGM2 and PGM2L1 belong 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 = 487

 Score = 27.5 bits (62), Expect = 1.2
 Identities = 24/93 (25%), Positives = 33/93 (35%), Gaps = 21/93 (22%)

Query: 15  LAVQSARMQIISENIANA---RTTGDTPGSDPYRRKTISFEEV---MHGSGGVRVKKI-- 66
            A+ S  ++ I E I +A            +    K +    V   +HG GG  V +   
Sbjct: 150 EALDSGLIKYIGEEIDDAYLEAVKKLLVNPELNEGKDLKI--VYTPLHGVGGKFVPRALK 207

Query: 67  --GVDQSTFVEE---FDPGHPVANASGIVKYPN 94
             G      VEE    DP  P       VK+PN
Sbjct: 208 EAGFTNVIVVEEQAEPDPDFPT------VKFPN 234


>gnl|CDD|133376 cd04176, Rap2, Rap2 subgroup.  The Rap2 subgroup is part of the
          Rap subfamily of the Ras family.  It consists of Rap2a,
          Rap2b, and Rap2c.  Both isoform 3 of the human
          mitogen-activated protein kinase kinase kinase kinase 4
          (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK)
          are putative effectors of Rap2 in mediating the
          activation of c-Jun N-terminal kinase (JNK) to regulate
          the actin cytoskeleton.  In human platelets, Rap2 was
          shown to interact with the cytoskeleton by binding the
          actin filaments.  In embryonic Xenopus development,
          Rap2 is necessary for the Wnt/beta-catenin signaling
          pathway.  The Rap2 interacting protein 9 (RPIP9) is
          highly expressed in human breast carcinomas and
          correlates with a poor prognosis, suggesting a role for
          Rap2 in breast cancer oncogenesis.  Rap2b, but not
          Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human
          red blood cells, where it is believed to be involved in
          vesiculation.  A number of additional effector proteins
          for Rap2 have been identified, including the RalGEFs
          RalGDS, RGL, and Rlf, which also interact with Rap1 and
          Ras.  Most Ras proteins contain a lipid modification
          site at the C-terminus, with a typical sequence motif
          CaaX, where a = an aliphatic amino acid and X = any
          amino acid.  Lipid binding is essential for membrane
          attachment, a key feature of most Ras proteins.  Due to
          the presence of truncated sequences in this CD, the
          lipid modification site is not available for
          annotation.
          Length = 163

 Score = 25.6 bits (56), Expect = 4.2
 Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 2/31 (6%)

Query: 51 FEEVMHGSGGVRVKKIGVD--QSTFVEEFDP 79
          ++ V+ GSGGV    + V     TF+E++DP
Sbjct: 2  YKVVVLGSGGVGKSALTVQFVSGTFIEKYDP 32


>gnl|CDD|133336 cd04136, Rap_like, Rap-like subfamily.  The Rap subfamily
          consists of the Rap1, Rap2, and RSR1.  Rap subfamily
          proteins perform different cellular functions,
          depending on the isoform and its subcellular
          localization. For example, in rat salivary gland,
          neutrophils, and platelets, Rap1 localizes to secretory
          granules and is believed to regulate exocytosis or the
          formation of secretory granules.  Rap1 has also been
          shown to localize in the Golgi of rat fibroblasts,
          zymogen granules, plasma membrane, and microsomal
          membrane of the pancreatic acini, as well as in the
          endocytic compartment of skeletal muscle cells and
          fibroblasts.   Rap1 localizes in the nucleus of human
          oropharyngeal squamous cell carcinomas (SCCs) and cell
          lines.  Rap1 plays a role in phagocytosis by
          controlling the binding of adhesion receptors
          (typically integrins) to their ligands.  In yeast, Rap1
          has been implicated in multiple functions, including
          activation and silencing of transcription and
          maintenance of telomeres.  Rap2 is involved in multiple
          functions, including activation of c-Jun N-terminal
          kinase (JNK) to regulate the actin cytoskeleton and
          activation of the Wnt/beta-catenin signaling pathway in
          embryonic Xenopus.  A number of effector proteins for
          Rap2 have been identified, including isoform 3 of the
          human mitogen-activated protein kinase kinase kinase
          kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase
          (TNIK), and the RalGEFs RalGDS, RGL, and Rlf, which
          also interact with Rap1 and Ras. RSR1 is the fungal
          homolog of Rap1 and Rap2.  In budding yeasts, it is
          involved in selecting a site for bud growth, which
          directs the establishment of cell polarization.  The
          Rho family GTPase Cdc42 and its GEF, Cdc24, then
          establish an axis of polarized growth.  It is believed
          that Cdc42 interacts directly with RSR1 in vivo.  In
          filamentous fungi such as Ashbya gossypii, RSR1 is a
          key regulator of polar growth in the hypha.  Most Ras
          proteins contain a lipid modification site at the
          C-terminus, with a typical sequence motif CaaX, where a
          = an aliphatic amino acid and X = any amino acid.
          Lipid binding is essential for membrane attachment, a
          key feature of most Ras proteins.  Due to the presence
          of truncated sequences in this CD, the lipid
          modification site is not available for annotation.
          Length = 163

 Score = 25.3 bits (56), Expect = 4.7
 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 2/31 (6%)

Query: 51 FEEVMHGSGGVRVKKIGVD--QSTFVEEFDP 79
          ++ V+ GSGGV    + V   Q  FVE++DP
Sbjct: 2  YKVVVLGSGGVGKSALTVQFVQGIFVEKYDP 32


>gnl|CDD|37958 KOG2747, KOG2747, KOG2747, Histone acetyltransferase (MYST family)
           [Chromatin structure and dynamics].
          Length = 396

 Score = 25.4 bits (55), Expect = 4.7
 Identities = 8/16 (50%), Positives = 11/16 (68%)

Query: 39  PGSDPYRRKTISFEEV 54
           PG++ YR+  IS  EV
Sbjct: 187 PGNEIYRKGNISVFEV 202


>gnl|CDD|34398 COG4787, FlgF, Flagellar basal body rod protein [Cell motility
          and secretion].
          Length = 251

 Score = 25.3 bits (55), Expect = 5.7
 Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 1  MDYLIASAHIANSGLAVQSARMQIISENIANARTTG 36
          MD+ I +A  A S L  Q     + + N+ANA TTG
Sbjct: 1  MDHAIYTAMGAASQLLEQ---QAVTANNLANASTTG 33



 Score = 24.9 bits (54), Expect = 7.1
 Identities = 28/119 (23%), Positives = 47/119 (39%), Gaps = 7/119 (5%)

Query: 20  ARMQIISENIANARTTGDTPGS----DPYRRKTISFEEVMHGSGGV-RVKKIGVDQSTFV 74
           A++ I ++   +A   GD   +       +    + +EV  G  G+ R+          V
Sbjct: 133 AKVTIAADGTISALNPGDPANTVAVVGRLKLVQATGQEVQRGDDGLFRLTAETQQPRGQV 192

Query: 75  EEFDPGHPVANASGIVKYPNVNVLVETADMRETNRLYMANLQTIKQSHDMMTTTLDLLR 133
            + DP   V   SG ++  NVN + E  DM    R +   ++ I  + D       LLR
Sbjct: 193 LKADPSVRVM--SGALEGSNVNAVEEMTDMISLARQFEMQMKMISTADDNAGAANQLLR 249


>gnl|CDD|145166 pfam01853, MOZ_SAS, MOZ/SAS family.  This region of these
          proteins has been suggested to be homologous to
          acetyltransferases.
          Length = 189

 Score = 24.5 bits (54), Expect = 8.3
 Identities = 8/16 (50%), Positives = 11/16 (68%)

Query: 39 PGSDPYRRKTISFEEV 54
          PG++ YR+  IS  EV
Sbjct: 5  PGNEIYRKGNISVFEV 20


  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    0.130    0.359 

Gapped
Lambda     K      H
   0.267   0.0747    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,480,540
Number of extensions: 68663
Number of successful extensions: 140
Number of sequences better than 10.0: 1
Number of HSP's gapped: 136
Number of HSP's successfully gapped: 21
Length of query: 134
Length of database: 6,263,737
Length adjustment: 84
Effective length of query: 50
Effective length of database: 4,448,581
Effective search space: 222429050
Effective search space used: 222429050
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: 52 (23.8 bits)