RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 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|178998 PRK00392, rpoZ, DNA-directed RNA polymerase subunit omega;
          Reviewed.
          Length = 69

 Score = 96.9 bits (242), Expect = 1e-21
 Identities = 39/69 (56%), Positives = 48/69 (69%)

Query: 1  MARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSP 60
          MAR T+ED ++KVDNR+ LVLLA+ R R L  GAKP VD   DK  V+ALREIA G ++ 
Sbjct: 1  MARPTIEDLLEKVDNRYELVLLAAKRARQLRAGAKPPVDKSSDKPVVIALREIAEGKVTY 60

Query: 61 DDLEEDFIH 69
          + LEE  I 
Sbjct: 61 EILEEVEIE 69


>gnl|CDD|161999 TIGR00690, rpoZ, DNA-directed RNA polymerase, omega subunit.  The
          trusted cutoff excludes archaeal homologs but captures
          some organellar sequences.
          Length = 59

 Score = 55.2 bits (133), Expect = 5e-09
 Identities = 26/59 (44%), Positives = 38/59 (64%), Gaps = 1/59 (1%)

Query: 2  ARTTVEDCIDKVDNRFLLVLLASHRTRHLSQGAKPTVDVGK-DKNTVVALREIASGTLS 59
          AR T+ED + K+ +R+ LVL+A+ R R L       +   + DK TV+ALREIA+G +S
Sbjct: 1  ARPTIEDAMKKIGSRYDLVLVAARRARQLQLKGTDPIVPEENDKPTVIALREIAAGLVS 59


>gnl|CDD|184839 PRK14829, PRK14829, undecaprenyl pyrophosphate synthase;
           Provisional.
          Length = 243

 Score = 27.1 bits (60), Expect = 1.2
 Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 5/33 (15%)

Query: 51  REIASGTLSPDDLEEDFIHSLQKHVEIDEPDSP 83
           RE+  G +S D + E  I        +  PD P
Sbjct: 157 REVRDGKISGDRVTEKMISDH-----LYNPDMP 184


>gnl|CDD|183725 PRK12755, PRK12755, phospho-2-dehydro-3-deoxyheptonate aldolase;
          Provisional.
          Length = 353

 Score = 26.0 bits (58), Expect = 2.7
 Identities = 6/19 (31%), Positives = 11/19 (57%)

Query: 2  ARTTVEDCIDKVDNRFLLV 20
          +R  + D +   D+R L+V
Sbjct: 40 SRQAIADILHGRDDRLLVV 58


>gnl|CDD|184947 PRK14985, PRK14985, maltodextrin phosphorylase; Provisional.
          Length = 798

 Score = 25.8 bits (57), Expect = 2.8
 Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 30  LSQGAKPTVDVGKDKNTVVALREIASGTLSPDDLE--EDFIHSLQK 73
           L++G  P     KDK     L+E+ SG  S  D    +  +HSL++
Sbjct: 690 LAKGYDPVKWRKKDKVLDAVLKELESGKYSDGDKHAFDQMLHSLKQ 735


>gnl|CDD|150933 pfam10337, DUF2422, Protein of unknown function (DUF2422).  This is
           a family of proteins conserved in fungi. The function is
           not known. This family is the C-terminal half of some
           member proteins which contain the DUF2421 pfam10334
           domain at their N-terminus.
          Length = 448

 Score = 25.4 bits (56), Expect = 4.3
 Identities = 7/20 (35%), Positives = 9/20 (45%)

Query: 51  REIASGTLSPDDLEEDFIHS 70
            E + G LS DDL+      
Sbjct: 280 LEFSYGRLSADDLKTIRRLL 299


>gnl|CDD|165718 PLN00150, PLN00150, potassium ion transporter family protein;
           Provisional.
          Length = 779

 Score = 24.8 bits (54), Expect = 5.0
 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 61  DDLEEDFIHSLQKHVEID--EPDSPTENSDFSWHKPEALSFGQMSEGD 106
           D+ E+  I SL++ +EI+     S  E+   SW  PE L     S G 
Sbjct: 625 DNFEQLLIASLERFIEIESFREQSDLESMAASW-TPEELMGEGNSVGS 671


>gnl|CDD|162992 TIGR02739, TraF, type-F conjugative transfer system pilin assembly
           protein TraF.  This protein is part of a large group of
           proteins involved in conjugative transfer of plasmid
           DNA, specifically the F-type system. This protein has
           been predicted to contain a thioredoxin fold and has
           been shown to be localized to the periplasm. Unlike the
           related protein TrbB (TIGR02738), TraF does not contain
           a conserved pair of cysteines and has been shown not to
           function as a thiol disulfide isomerase by
           complementation of an Ecoli DsbA defect. The protein is
           believed to be involved in pilin assembly. Even more
           closely related than TrbB is a clade of genes
           (TIGR02740) which do contain the CXXC motif, but it is
           unclear whether these genes are involved in type-F
           conjugation systems per se.
          Length = 256

 Score = 25.1 bits (55), Expect = 5.4
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 92  HKPEALSFGQMSEGDLLEGINNIVTPDKRDD 122
            K   L++G +S+ +L E I N++T  KR D
Sbjct: 225 QKMSPLAYGFISQDELKERILNVLTQFKRPD 255


>gnl|CDD|184096 PRK13505, PRK13505, formate--tetrahydrofolate ligase;
          Provisional.
          Length = 557

 Score = 24.8 bits (55), Expect = 5.5
 Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 7/25 (28%)

Query: 35 KPTVDVG-------KDKNTVVALRE 52
          K TV VG         K TV+ALRE
Sbjct: 72 KSTVTVGLGDALNKIGKKTVIALRE 96


>gnl|CDD|150974 pfam10390, ELL, RNA polymerase II elongation factor ELL.  ELL is
          a family of RNA polymerase II elongation factors. It is
          bound stably to elongation-associated factors 1 and 2,
          EAFs, and together these act as a strong regulator of
          transcription activity. by direct interaction with Pol
          II. ELL binds to pol II on its own but the affinity is
          greatly increased by the cooperation of EAF. Some
          members carry an Occludin domain pfam07303 just
          downstream. There is no S. cerevisiae member.
          Length = 285

 Score = 24.7 bits (54), Expect = 6.3
 Identities = 8/23 (34%), Positives = 14/23 (60%)

Query: 71 LQKHVEIDEPDSPTENSDFSWHK 93
           Q +++I  PDSP+    FS++ 
Sbjct: 53 NQGYIKIPSPDSPSSVRTFSFYL 75


>gnl|CDD|162698 TIGR02093, P_ylase, glycogen/starch/alpha-glucan phosphorylases.
           This family consists of phosphorylases. Members use
           phosphate to break alpha 1,4 linkages between pairs of
           glucose residues at the end of long glucose polymers,
           releasing alpha-D-glucose 1-phosphate. The nomenclature
           convention is to preface the name according to the
           natural substrate, as in glycogen phosphorylase, starch
           phosphorylase, maltodextrin phosphorylase, etc. Name
           differences among these substrates reflect differences
           in patterns of branching with alpha 1,6 linkages.
           Members include allosterically regulated and unregulated
           forms. A related family, TIGR02094, contains examples
           known to act well on particularly small alpha 1,4
           glucans, as may be found after import from exogenous
           sources.
          Length = 794

 Score = 24.5 bits (54), Expect = 7.1
 Identities = 18/63 (28%), Positives = 22/63 (34%), Gaps = 2/63 (3%)

Query: 14  DNRFLLVLLASHRTRHLSQGAKPTVDVGKDKNTVVALREIASGTLSPDD--LEEDFIHSL 71
           +N F+  L          +G  P      D      L  I+SGT SP D  L      SL
Sbjct: 672 ENIFIFGLTVEEVEALREKGYNPREYYEADPELKRVLDLISSGTFSPGDPGLFRPLYDSL 731

Query: 72  QKH 74
             H
Sbjct: 732 LNH 734


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.313    0.132    0.380 

Gapped
Lambda     K      H
   0.267   0.0622    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,026,041
Number of extensions: 117727
Number of successful extensions: 172
Number of sequences better than 10.0: 1
Number of HSP's gapped: 171
Number of HSP's successfully gapped: 20
Length of query: 122
Length of database: 5,994,473
Length adjustment: 82
Effective length of query: 40
Effective length of database: 4,222,617
Effective search space: 168904680
Effective search space used: 168904680
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 (23.7 bits)