RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9733
         (86 letters)



>gnl|CDD|176117 cd08426, PBP2_LTTR_like_5, The C-terminal substrate binding domain
           of an uncharacterized LysR-type transcriptional
           regulator, contains the type 2 periplasmic binding fold.
            LysR-transcriptional regulators comprise the largest
           family of prokaryotic transcription factor. Homologs of
           some of LTTRs with similar domain organizations are also
           found in the archaea and eukaryotic organisms. The LTTRs
           are composed of two functional domains joined by a
           linker helix involved in oligomerization: an N-terminal
           HTH (helix-turn-helix) domain, which is responsible for
           the DNA-binding specificity, and a C-terminal
           substrate-binding domain, which is structurally
           homologous to the type 2 periplasmic binding proteins.
           As also observed in the periplasmic binding proteins,
           the C-terminal domain of the bacterial transcriptional
           repressor undergoes a conformational change upon
           substrate binding which in turn changes the DNA binding
           affinity of the repressor.  The genes controlled by the
           LTTRs have diverse functional roles including amino acid
           biosynthesis, CO2 fixation, antibiotic resistance,
           degradation of aromatic compounds, nodule formation of
           nitrogen-fixing bacteria, and synthesis of virulence
           factors, to a name a few.  This substrate-binding domain
           shows significant homology to the type 2 periplasmic
           binding proteins (PBP2), which are responsible for the
           uptake of a variety of substrates such as phosphate,
           sulfate, polysaccharides, lysine/arginine/ornithine, and
           histidine. The PBP2 bind their ligand in the cleft
           between these domains in a manner resembling a Venus
           flytrap. After binding their specific ligand with high
           affinity, they can interact with a cognate membrane
           transport complex comprised of two integral membrane
           domains and two cytoplasmically located ATPase domains.
           This interaction triggers the ligand translocation
           across the cytoplasmic membrane energized by ATP
           hydrolysis.
          Length = 199

 Score = 26.5 bits (59), Expect = 1.3
 Identities = 8/30 (26%), Positives = 13/30 (43%)

Query: 57  LRQLFRILFRTLNHQYDYLYHNNSSSLLLE 86
           LRQ+    F     Q + +  +NS   L +
Sbjct: 109 LRQILDAAFARAGVQLEPVLISNSIETLKQ 138


>gnl|CDD|234675 PRK00170, PRK00170, azoreductase; Reviewed.
          Length = 201

 Score = 26.4 bits (59), Expect = 1.5
 Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 2/32 (6%)

Query: 11  EQIVARGRLVMVAPSYWHNPSFPAEFAMYLNY 42
           E+ +A  ++V+ AP Y  N S P +   Y++ 
Sbjct: 82  EEFLAADKIVIAAPMY--NFSIPTQLKAYIDL 111


>gnl|CDD|226115 COG3587, COG3587, Restriction endonuclease [Defense mechanisms].
          Length = 985

 Score = 26.3 bits (58), Expect = 2.0
 Identities = 8/30 (26%), Positives = 16/30 (53%)

Query: 57  LRQLFRILFRTLNHQYDYLYHNNSSSLLLE 86
             + F+ L+  +NH+    Y  +S +L+ E
Sbjct: 671 NFKEFKALWEKINHKAVLQYQIDSEALIDE 700


>gnl|CDD|165211 PHA02882, PHA02882, putative serine/threonine kinase; Provisional.
          Length = 294

 Score = 25.7 bits (56), Expect = 2.9
 Identities = 8/24 (33%), Positives = 13/24 (54%)

Query: 38  MYLNYCRGLRFEEAPDYMYLRQLF 61
            ++     L +EE PDY  L ++F
Sbjct: 270 DFIECVTKLSYEEKPDYDALIKIF 293


>gnl|CDD|213289 cd05922, FACL_like_6, Uncharacterized subfamily of fatty acid CoA
           ligase (FACL).  Fatty acyl-CoA ligases catalyze the
           ATP-dependent activation of fatty acids in a two-step
           reaction. The carboxylate substrate first reacts with
           ATP to form an acyl-adenylate intermediate, which then
           reacts with CoA to produce an acyl-CoA ester. This is a
           required step before free fatty acids can participate in
           most catabolic and anabolic reactions.
          Length = 350

 Score = 25.7 bits (57), Expect = 3.3
 Identities = 8/19 (42%), Positives = 12/19 (63%), Gaps = 2/19 (10%)

Query: 12  QIVARGRLVMVAPSYWHNP 30
           ++V RG  VM    YW++P
Sbjct: 199 ELVHRGANVMKG--YWNDP 215


>gnl|CDD|128341 smart00026, EPEND, Ependymins.  Ependymins are the predominant
           proteins in the cerebrospinal fluid (CSF) of teleost
           fish. They have been implicated in the neurochemistry of
           memory and neuronal regeneration. They are glycoproteins
           of about 200 amino acids that can bind calcium. Four
           cysteines are conserved that probably form disulfide
           bonds.
          Length = 191

 Score = 25.2 bits (55), Expect = 4.0
 Identities = 10/20 (50%), Positives = 11/20 (55%)

Query: 42  YCRGLRFEEAPDYMYLRQLF 61
           YC G+  EEAPD      LF
Sbjct: 170 YCEGVALEEAPDDHSFFDLF 189


>gnl|CDD|165270 PHA02965, PHA02965, hypothetical protein; Provisional.
          Length = 466

 Score = 25.3 bits (55), Expect = 4.2
 Identities = 6/19 (31%), Positives = 13/19 (68%)

Query: 66  RTLNHQYDYLYHNNSSSLL 84
           + LN   D ++H+N+++L 
Sbjct: 280 KELNANIDKIFHHNNNTLF 298


>gnl|CDD|185500 PTZ00175, PTZ00175, diphthine synthase; Provisional.
          Length = 270

 Score = 24.9 bits (55), Expect = 5.2
 Identities = 8/27 (29%), Positives = 12/27 (44%), Gaps = 4/27 (14%)

Query: 41  NYCRGLRFEEAPDYMY----LRQLFRI 63
           N  +G +  E P YM     + QL  +
Sbjct: 176 NLMKGRKIYEPPRYMTINQAIEQLLEV 202


>gnl|CDD|236042 PRK07525, PRK07525, sulfoacetaldehyde acetyltransferase; Validated.
          Length = 588

 Score = 25.0 bits (55), Expect = 6.2
 Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 3/25 (12%)

Query: 22  VAPSYWHNPSFPAEFAMY---LNYC 43
           VA  Y HN +FP    ++   L Y 
Sbjct: 231 VACGYLHNDAFPGSHPLWVGPLGYN 255


>gnl|CDD|216073 pfam00709, Adenylsucc_synt, Adenylosuccinate synthetase. 
          Length = 420

 Score = 24.8 bits (55), Expect = 7.5
 Identities = 10/34 (29%), Positives = 14/34 (41%)

Query: 44  RGLRFEEAPDYMYLRQLFRILFRTLNHQYDYLYH 77
           RG+R  +  D   LR+    L    N   + LY 
Sbjct: 142 RGIRVGDLLDEEVLREKLEQLLEEKNAILEKLYG 175


>gnl|CDD|226142 COG3615, TehB, Uncharacterized protein/domain, possibly involved
          in tellurite resistance [Inorganic ion transport and
          metabolism].
          Length = 99

 Score = 23.9 bits (52), Expect = 8.2
 Identities = 4/22 (18%), Positives = 6/22 (27%)

Query: 8  VREEQIVARGRLVMVAPSYWHN 29
            E       +  +  P  WH 
Sbjct: 59 EPEHVFSIEAQFPVFPPQAWHR 80


>gnl|CDD|224434 COG1517, COG1517, CRISPR system related protein [Defense
           mechanisms].
          Length = 406

 Score = 24.3 bits (53), Expect = 9.6
 Identities = 9/41 (21%), Positives = 12/41 (29%), Gaps = 9/41 (21%)

Query: 20  VMVAPSYW---------HNPSFPAEFAMYLNYCRGLRFEEA 51
           V+V P             N  F   +  YL    G +  E 
Sbjct: 86  VIVLPGKGSFSGKPDFDINHLFGYIYYHYLLTLEGEKKIEI 126


  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
   0.327    0.139    0.447 

Gapped
Lambda     K      H
   0.267   0.0616    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,591,019
Number of extensions: 374793
Number of successful extensions: 427
Number of sequences better than 10.0: 1
Number of HSP's gapped: 427
Number of HSP's successfully gapped: 21
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.4 bits)