RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy1385
         (69 letters)



>gnl|CDD|225432 COG2877, KdsA, 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate
           synthase [Cell envelope biogenesis, outer membrane].
          Length = 279

 Score = 27.3 bits (61), Expect = 0.52
 Identities = 8/15 (53%), Positives = 11/15 (73%)

Query: 53  NDQAILCESGCNFWY 67
           N++ ILCE G +F Y
Sbjct: 159 NNKVILCERGASFGY 173


>gnl|CDD|235363 PRK05198, PRK05198, 2-dehydro-3-deoxyphosphooctonate aldolase;
           Provisional.
          Length = 264

 Score = 26.6 bits (60), Expect = 0.76
 Identities = 9/16 (56%), Positives = 12/16 (75%)

Query: 53  NDQAILCESGCNFWYH 68
           ND+ ILCE G +F Y+
Sbjct: 152 NDKIILCERGTSFGYN 167


>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
           Provisional.
          Length = 475

 Score = 26.7 bits (59), Expect = 0.78
 Identities = 14/41 (34%), Positives = 17/41 (41%), Gaps = 5/41 (12%)

Query: 2   TPGG---PGFPNTKPMPVCAGKIYPENQAMVFNPQNPNAPP 39
           T  G   P  P + P P   G+  P N  + F PQ   A P
Sbjct: 129 TATGEPVPQMPASPPGP--EGEPQPGNTPVSFPPQGSVAVP 167


>gnl|CDD|130429 TIGR01362, KDO8P_synth, 3-deoxy-8-phosphooctulonate synthase.  This
           model describes 3-deoxy-8-phosphooctulonate synthase.
           Alternate names include 2-dehydro-3-deoxyphosphooctonate
           aldolase, 3-deoxy-d-manno-octulosonic acid 8-phosphate
           and KDO-8 phosphate synthetase. It catalyzes the aldol
           condensation of phosphoenolpyruvate with D-arabinose
           5-phosphate: phosphoenolpyruvate + D-arabinose
           5-phosphate + H2O = 2-dehydro-3-deoxy-D-octonate
           8-phosphate + phosphate In Gram-negative bacteria, this
           is the first step in the biosynthesis of
           3-deoxy-D-manno-octulosonate, part of the
           oligosaccharide core of lipopolysaccharide [Cell
           envelope, Biosynthesis and degradation of surface
           polysaccharides and lipopolysaccharides].
          Length = 258

 Score = 26.6 bits (59), Expect = 0.99
 Identities = 7/15 (46%), Positives = 9/15 (60%)

Query: 53  NDQAILCESGCNFWY 67
           N   +LCE G +F Y
Sbjct: 144 NKNILLCERGTSFGY 158


>gnl|CDD|201356 pfam00628, PHD, PHD-finger.  PHD folds into an interleaved type
          of Zn-finger chelating 2 Zn ions in a similar manner to
          that of the RING and FYVE domains. Several PHD fingers
          have been identified as binding modules of methylated
          histone H3.
          Length = 51

 Score = 25.1 bits (55), Expect = 1.3
 Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 2/26 (7%)

Query: 43 CGICHKEVHDNDQAILCESGCNFWYH 68
          C +C K   D +  +LC+ GC+ W+H
Sbjct: 2  CAVCGKVDDDGEL-LLCD-GCDRWFH 25


>gnl|CDD|237105 PRK12457, PRK12457, 2-dehydro-3-deoxyphosphooctonate aldolase;
           Provisional.
          Length = 281

 Score = 26.2 bits (58), Expect = 1.3
 Identities = 9/15 (60%), Positives = 11/15 (73%)

Query: 53  NDQAILCESGCNFWY 67
           ND+ ILCE G +F Y
Sbjct: 158 NDRVILCERGSSFGY 172


>gnl|CDD|171793 PRK12880, PRK12880, 3-oxoacyl-(acyl carrier protein) synthase III;
           Reviewed.
          Length = 353

 Score = 25.7 bits (56), Expect = 1.8
 Identities = 7/24 (29%), Positives = 12/24 (50%)

Query: 31  NPQNPNAPPIYPCGICHKEVHDND 54
           +P+N N  PI+  G+    +   D
Sbjct: 156 HPKNMNLAPIFGDGVSATLIEKTD 179


>gnl|CDD|215304 PLN02554, PLN02554, UDP-glycosyltransferase family protein.
          Length = 481

 Score = 25.5 bits (56), Expect = 2.0
 Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 2/33 (6%)

Query: 24  ENQAM-VFNPQNPNAPPIYPCG-ICHKEVHDND 54
           E QA+  F+  + + PP+YP G + H E   +D
Sbjct: 223 EPQALKFFSGSSGDLPPVYPVGPVLHLENSGDD 255


>gnl|CDD|218658 pfam05616, Neisseria_TspB, Neisseria meningitidis TspB protein.
           This family consists of several Neisseria meningitidis
           TspB virulence factor proteins.
          Length = 502

 Score = 24.6 bits (53), Expect = 4.6
 Identities = 13/41 (31%), Positives = 17/41 (41%), Gaps = 2/41 (4%)

Query: 1   MTPGGPGFPNTKPMPVCAGKIYP-ENQAMVFNPQ-NPNAPP 39
           +TPG    P  +P+P  +    P  N     NP   PN  P
Sbjct: 319 LTPGSAEAPEAQPLPEVSPAENPANNPNPRENPGTRPNPEP 359


>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA
           processing and modification].
          Length = 1175

 Score = 24.5 bits (53), Expect = 4.7
 Identities = 7/41 (17%), Positives = 14/41 (34%), Gaps = 6/41 (14%)

Query: 24  ENQAMVFNPQNPNAPPIYPC------GICHKEVHDNDQAIL 58
           ++   V NP + N P            +     +D+  + L
Sbjct: 260 DSNNNVINPVSDNVPSRDMNDSRNVENVRPVRSNDHMNSFL 300


>gnl|CDD|180142 PRK05578, PRK05578, cytidine deaminase; Validated.
          Length = 131

 Score = 24.1 bits (53), Expect = 5.4
 Identities = 5/9 (55%), Positives = 6/9 (66%)

Query: 38 PPIYPCGIC 46
           P+ PCG C
Sbjct: 81 EPLSPCGRC 89


>gnl|CDD|214584 smart00249, PHD, PHD zinc finger.  The plant homeodomain (PHD)
          finger is a C4HC3 zinc-finger-like motif found in
          nuclear proteins thought to be involved in epigenetics
          and chromatin-mediated transcriptional regulation. The
          PHD finger binds two zinc ions using the so-called
          'cross-brace' motif and is thus structurally related to
          the RING finger and the FYVE finger. It is not yet
          known if PHD fingers have a common molecular function.
          Several reports suggest that it can function as a
          protein-protein interacton domain and it was recently
          demonstrated that the PHD finger of p300 can cooperate
          with the adjacent BROMO domain in nucleosome binding in
          vitro. Other reports suggesting that the PHD finger is
          a ubiquitin ligase have been refuted as these domains
          were RING fingers misidentified as PHD fingers.
          Length = 47

 Score = 23.3 bits (50), Expect = 5.7
 Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 2/26 (7%)

Query: 43 CGICHKEVHDNDQAILCESGCNFWYH 68
          C +C K   D  + + C+ GC+ WYH
Sbjct: 2  CSVCGKP-DDGGELLQCD-GCDRWYH 25


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.321    0.142    0.511 

Gapped
Lambda     K      H
   0.267   0.0598    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,507,641
Number of extensions: 240631
Number of successful extensions: 252
Number of sequences better than 10.0: 1
Number of HSP's gapped: 251
Number of HSP's successfully gapped: 17
Length of query: 69
Length of database: 10,937,602
Length adjustment: 39
Effective length of query: 30
Effective length of database: 9,207,796
Effective search space: 276233880
Effective search space used: 276233880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.5 bits)