RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780937|ref|YP_003065350.1| DNA-directed RNA polymerase
subunit omega [Candidatus Liberibacter asiaticus str. psy62]
         (122 letters)



>gnl|CDD|31944 COG1758, RpoZ, DNA-directed RNA polymerase, subunit K/omega
          [Transcription].
          Length = 74

 Score = 76.1 bits (187), Expect = 2e-15
 Identities = 40/74 (54%), Positives = 50/74 (67%), Gaps = 2/74 (2%)

Query: 1  MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDV--GKDKNTVVALREIASGTL 58
          MAR T+ED +DKV NR+ LV++A+ R R L+ GA P VD    KDK  V+ALREIA G +
Sbjct: 1  MARPTIEDLLDKVGNRYELVVVAAKRARQLAAGAPPLVDDEENKDKPVVIALREIAEGKI 60

Query: 59 SPDDLEEDFIHSLQ 72
            + L E  IHSLQ
Sbjct: 61 PIEILRELLIHSLQ 74


>gnl|CDD|144692 pfam01192, RNA_pol_Rpb6, RNA polymerase Rpb6.  Rpb6 is an
          essential subunit in the eukaryotic polymerases Pol I,
          II and III. This family also contains the bacterial
          equivalent to Rpb6, the omega subunit. Rpb6 and omega
          are structurally conserved and both function in
          polymerase assembly.
          Length = 57

 Score = 56.5 bits (137), Expect = 2e-09
 Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 7  EDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVD-VGKDKNTVVALREIASGTLSPD 61
          E    K  NR+ L  + + R + LS GA P VD   + K  V+AL EIA G + P+
Sbjct: 1  ERLTSKYLNRYELARIIAKRAKQLSYGAPPLVDEESEIKPVVIALEEIADGKIPPE 56


>gnl|CDD|144074 pfam00343, Phosphorylase, Carbohydrate phosphorylase.  The members
           of this family catalyse the formation of glucose
           1-phosphate from one of the following polyglucoses;
           glycogen, starch, glucan or maltodextrin.
          Length = 712

 Score = 26.2 bits (58), Expect = 2.2
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 2/63 (3%)

Query: 14  DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLE--EDFIHSL 71
           +N F+  L A        +G +      KD      L +I SG  SP+D +   D + SL
Sbjct: 589 ENIFIFGLTAEEVEALRKKGYRSREYYKKDPRLRQVLDQIISGFFSPEDPDRFRDILDSL 648

Query: 72  QKH 74
           Q  
Sbjct: 649 QGG 651


>gnl|CDD|143454 cd07136, ALDH_YwdH-P39616, Bacillus subtilis aldehyde dehydrogenase
           ywdH-like.  Uncharacterized Bacillus subtilis ywdH
           aldehyde dehydrogenase (locus P39616)  most closely
           related to the ALDHs and fatty ALDHs of families 3 and
           14, and similar sequences, are included in this CD.
          Length = 449

 Score = 25.9 bits (58), Expect = 2.5
 Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 14/71 (19%)

Query: 33  GAKPTVDVGKDKNTVVALREIASGTL--------SPD------DLEEDFIHSLQKHVEID 78
           G K    V +D N  +A + I  G          +PD       ++E FI  L++ ++  
Sbjct: 208 GGKSPCIVDEDANLKLAAKRIVWGKFLNAGQTCVAPDYVLVHESVKEKFIKELKEEIKKF 267

Query: 79  EPDSPTENSDF 89
             + P E+ D+
Sbjct: 268 YGEDPLESPDY 278


>gnl|CDD|34199 COG4555, NatA, ABC-type Na+ transport system, ATPase component
           [Energy production and conversion / Inorganic ion
           transport and metabolism].
          Length = 245

 Score = 25.3 bits (55), Expect = 4.1
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 3/59 (5%)

Query: 1   MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGK---DKNTVVALREIASG 56
           ++R  ++  I ++  R  L+     R    S G K  V + +      +++ L E  SG
Sbjct: 105 LSRKEIKARIAELSKRLQLLEYLDRRVGEFSTGMKQKVAIARALVHDPSILVLDEPTSG 163


>gnl|CDD|37454 KOG2243, KOG2243, KOG2243, Ca2+ release channel (ryanodine receptor)
            [Signal transduction mechanisms].
          Length = 5019

 Score = 24.6 bits (53), Expect = 7.6
 Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 5/37 (13%)

Query: 60   PDDLEE---DFIHSLQKH--VEIDEPDSPTENSDFSW 91
            P+++ +   DF   L  H  +E+DE +   E  D S 
Sbjct: 2001 PEEIRDELLDFHEDLLLHCGIELDEDEEEDEEEDLSI 2037


>gnl|CDD|146797 pfam04347, FliO, Flagellar biosynthesis protein, FliO.  FliO is
          an essential component of the flagellum-specific
          protein export apparatus. It is an integral membrane
          protein. Its precise molecular function is unknown.
          Length = 84

 Score = 24.5 bits (54), Expect = 8.1
 Identities = 5/25 (20%), Positives = 10/25 (40%)

Query: 12 KVDNRFLLVLLASHRTRHLSQGAKP 36
          +V  + LL+ +   +   L     P
Sbjct: 36 EVGGKQLLLGVTPQQITLLHTLDTP 60


>gnl|CDD|133201 cd05070, PTKc_Fyn_Yrk, Catalytic domain of the Protein Tyrosine
          Kinases, Fyn and Yrk.  Protein Tyrosine Kinase (PTK)
          family; Fyn and Yrk kinases; catalytic (c) domain. The
          PTKc family is part of a larger superfamily that
          includes the catalytic domains of other kinases such as
          protein serine/threonine kinases, RIO kinases, and
          phosphoinositide 3-kinase (PI3K). PTKs catalyze the
          transfer of the gamma-phosphoryl group from ATP to
          tyrosine (tyr) residues in protein substrates. Fyn and
          Yrk are members of the Src subfamily of proteins, which
          are cytoplasmic (or non-receptor) tyr kinases. Src
          kinases contain an N-terminal SH4 domain with a
          myristoylation site, followed by SH3 and SH2 domains, a
          tyr kinase domain, and a regulatory C-terminal region
          containing a conserved tyr. They are activated by
          autophosphorylation at the tyr kinase domain, but are
          negatively regulated by phosphorylation at the
          C-terminal tyr by Csk (C-terminal Src Kinase). Src
          proteins are involved in signaling pathways that
          regulate cytokine and growth factor responses,
          cytoskeleton dynamics, cell proliferation, survival,
          and differentiation. Fyn, together with Lck, plays a
          critical role in T-cell signal transduction by
          phosphorylating ITAM (immunoreceptor tyr activation
          motif) sequences on T-cell receptors, ultimately
          leading to the proliferation and differentiation of
          T-cells. In addition, Fyn is involved in the
          myelination of neurons, and is implicated in
          Alzheimer's and Parkinson's diseases. Yrk has been
          detected only in chickens. It is primarily found in
          neuronal and epithelial cells and in macrophages. It
          may play a role in inflammation and in response to
          injury.
          Length = 260

 Score = 24.6 bits (53), Expect = 8.1
 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)

Query: 45 NTVVALREIASGTLSPDD-LEEDFIHSLQKH 74
          NT VA++ +  GT+SP+  LEE  I    +H
Sbjct: 30 NTKVAVKTLKPGTMSPESFLEEAQIMKKLRH 60


  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
   0.313    0.132    0.380 

Gapped
Lambda     K      H
   0.267   0.0759    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,466,106
Number of extensions: 68680
Number of successful extensions: 128
Number of sequences better than 10.0: 1
Number of HSP's gapped: 126
Number of HSP's successfully gapped: 20
Length of query: 122
Length of database: 6,263,737
Length adjustment: 82
Effective length of query: 40
Effective length of database: 4,491,799
Effective search space: 179671960
Effective search space used: 179671960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (23.4 bits)