RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3923
         (73 letters)



>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
          Provisional.
          Length = 300

 Score = 67.5 bits (165), Expect = 2e-15
 Identities = 27/47 (57%), Positives = 34/47 (72%), Gaps = 2/47 (4%)

Query: 24 FAKDFIAGGVSAAVSKTAVAPIERVKLLLQVQHISKQISEEQ--RYK 68
          FA DF+ GG+SAA+SKTAVAPIERVK+L+Q Q    +I   +  RY 
Sbjct: 7  FATDFLMGGISAAISKTAVAPIERVKMLIQTQDSIPEIKSGKVPRYS 53


>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein. 
          Length = 96

 Score = 46.1 bits (110), Expect = 2e-08
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 4/49 (8%)

Query: 20 DPVAFAKDFIAGGVSAAVSKTAVAPIERVKLLLQVQHISKQISEEQRYK 68
           P++F    +AGG++ A++ T   P++ VK  LQ    S      ++YK
Sbjct: 1  SPLSFLASLLAGGIAGAIAATVTYPLDVVKTRLQ----SSAAGGSRKYK 45


>gnl|CDD|130412 TIGR01345, malate_syn_G, malate synthase G.  This model describes
           the G isozyme of malate synthase. Isocitrate synthase
           and malate synthase form the glyoxylate shunt, which
           generates additional TCA cycle intermediates [Energy
           metabolism, TCA cycle].
          Length = 721

 Score = 28.0 bits (62), Expect = 0.36
 Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 6/39 (15%)

Query: 1   MSKTVQKQ----EAPMPMAPALADPVAF--AKDFIAGGV 33
           M+K V +Q     A  PMA   A+  AF  A D I  G 
Sbjct: 661 MAKVVDQQNAGDPAYRPMAGNFANSCAFQAASDLIFLGT 699


>gnl|CDD|236918 PRK11498, bcsA, cellulose synthase catalytic subunit; Provisional.
          Length = 852

 Score = 27.3 bits (61), Expect = 0.64
 Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 7/59 (11%)

Query: 2   SKTVQKQ---EAPMPMAPALADPVAFA---KDFIAGGVSAAVSKTA-VAPIERVKLLLQ 53
           SK V++    E  MP A A  D   F+   +DF  GG+   ++  A +   ++V LLL+
Sbjct: 679 SKQVRRSHRVEMTMPAAIAREDGHLFSCTVQDFSDGGLGIKINGQAQLLEGQKVNLLLK 737


>gnl|CDD|238370 cd00728, malate_synt_G, Malate synthase G (MSG), monomeric enzyme
           present in some bacteria. In general, malate synthase
           catalyzes the Claisen condensation of glyoxylate and
           acetyl-CoA to malyl-CoA , which hydrolyzes to malate and
           CoA. This reaction is part of the glyoxylate cycle,
           which allows certain organisms to derive their carbon
           requirements from two-carbon compounds, by bypassing the
           two carboxylation steps of the citric acid cycle.
          Length = 712

 Score = 27.0 bits (60), Expect = 0.92
 Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 6/40 (15%)

Query: 1   MSKTVQKQEAP----MPMAPALADPVAF--AKDFIAGGVS 34
           M+K V +Q A      PMAP   D +AF  A D I  G  
Sbjct: 655 MAKVVDQQNAGDPSYRPMAPDFDDSIAFKAACDLIFQGKE 694


>gnl|CDD|100034 cd02203, PurL_repeat1, PurL subunit of the formylglycinamide
           ribonucleotide amidotransferase (FGAR-AT), first repeat.
           FGAR-AT catalyzes the ATP-dependent conversion of
           formylglycinamide ribonucleotide (FGAR) and glutamine to
           formylglycinamidine ribonucleotide (FGAM), ADP,
           phosphate, and glutamate in the fourth step of the
           purine biosynthetic pathway. In eukaryotes and
           Gram-negative bacteria, FGAR-AT is encoded by the purL
           gene as a multidomain protein with a molecular mass of
           about 140 kDa. In Gram-positive bacteria and archaea
           FGAR-AT is a complex of three proteins: PurS, PurL, and
           PurQ. PurL itself contains two tandem N- and C-terminal
           domains (four domains altogether). The N-terminal
           domains bind ATP and are related to the ATP-binding
           domains of HypE, ThiL, SelD and PurM.
          Length = 313

 Score = 25.5 bits (57), Expect = 2.3
 Identities = 9/28 (32%), Positives = 15/28 (53%)

Query: 14  MAPALADPVAFAKDFIAGGVSAAVSKTA 41
           +       +   +D  AGG+S+AVS+ A
Sbjct: 204 LEARETGLIVGIQDLGAGGLSSAVSEMA 231


>gnl|CDD|185214 PRK15314, PRK15314, outer membrane protein RatB; Provisional.
          Length = 2435

 Score = 25.6 bits (55), Expect = 2.4
 Identities = 13/35 (37%), Positives = 20/35 (57%)

Query: 5   VQKQEAPMPMAPALADPVAFAKDFIAGGVSAAVSK 39
           V  Q+  + +APA+ DPV  A D +   ++AA  K
Sbjct: 184 VLDQKFAVDIAPAVGDPVTLAADHLDESLNAAKVK 218


>gnl|CDD|235097 PRK02999, PRK02999, malate synthase G; Provisional.
          Length = 726

 Score = 25.5 bits (57), Expect = 2.6
 Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 6/35 (17%)

Query: 1   MSKTVQKQEA--P--MPMAPALADPVAF--AKDFI 29
           M+  V +Q A  P   PMAP   + +AF  A D +
Sbjct: 664 MAAVVDQQNAGDPAYRPMAPDFDNSIAFQAACDLV 698


>gnl|CDD|223124 COG0046, PurL, Phosphoribosylformylglycinamidine (FGAM) synthase,
           synthetase domain [Nucleotide transport and metabolism].
          Length = 743

 Score = 25.3 bits (56), Expect = 3.7
 Identities = 7/20 (35%), Positives = 11/20 (55%)

Query: 19  ADPVAFAKDFIAGGVSAAVS 38
              +   +D  AGG+S A+S
Sbjct: 270 TGLIKGIQDLGAGGLSCAIS 289


>gnl|CDD|216652 pfam01698, FLO_LFY, Floricaula / Leafy protein.  This family
           consists of various plant development proteins which are
           homologues of floricaula (FLO) and Leafy (LFY) proteins
           which are floral meristem identity proteins. Mutations
           in the sequences of these proteins affect flower and
           leaf development.
          Length = 382

 Score = 24.6 bits (54), Expect = 4.8
 Identities = 6/12 (50%), Positives = 11/12 (91%)

Query: 49  KLLLQVQHISKQ 60
           + L+QVQ+I+K+
Sbjct: 256 EFLIQVQNIAKE 267


>gnl|CDD|181644 PRK09088, PRK09088, acyl-CoA synthetase; Validated.
          Length = 488

 Score = 24.8 bits (54), Expect = 5.5
 Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 14  MAPALADPVAFAKDFIAGGVSAAVSKTAVAPIERVKLLL 52
           +A    D    A  FIA   +   + T   P ERV L+L
Sbjct: 104 VAAGRTDVEDLA-AFIASADALEPADTPSIPPERVSLIL 141


>gnl|CDD|223471 COG0394, Wzb, Protein-tyrosine-phosphatase [Signal transduction
          mechanisms].
          Length = 139

 Score = 24.5 bits (54), Expect = 5.6
 Identities = 18/69 (26%), Positives = 26/69 (37%), Gaps = 16/69 (23%)

Query: 13 PMAPALADPVAFAKDFIAGGV---SAAVSKTAVAPIER--VKLLLQV-----QHISKQIS 62
          PMA AL       +      V   SA        P +   V++L +       H SKQ++
Sbjct: 17 PMAEALL------RHLAPDNVEVDSAGTGGHPGEPPDPRAVEVLAEHGIDISGHRSKQLT 70

Query: 63 EEQRYKADF 71
          EE   + D 
Sbjct: 71 EEDFDEFDL 79


>gnl|CDD|131984 TIGR02938, nifL_nitrog, nitrogen fixation negative regulator NifL. 
           NifL is a modulator of the nitrogen fixation positive
           regulator protein NifA, and is therefore a negative
           regulator. It binds NifA. NifA and NifL are encoded by
           adjacent genes [Central intermediary metabolism,
           Nitrogen fixation, Regulatory functions, Protein
           interactions].
          Length = 494

 Score = 24.5 bits (53), Expect = 6.1
 Identities = 9/31 (29%), Positives = 15/31 (48%)

Query: 43  APIERVKLLLQVQHISKQISEEQRYKADFLK 73
              E+  LLL +  IS    E++R +   L+
Sbjct: 234 CAAEQPYLLLTIADISNLREEQERARLSALQ 264


>gnl|CDD|147867 pfam05946, TcpA, Toxin-coregulated pilus subunit TcpA.  This family
           consists of toxin-coregulated pilus subunit (TcpA)
           proteins from Vibrio cholerae and related sequences. The
           major virulence factors of toxigenic Vibrio cholerae are
           cholera toxin (CT), which is encoded by a lysogenic
           bacteriophage (CTXPhi), and toxin-coregulated pilus
           (TCP), an essential colonisation factor which is also
           the receptor for CTXPhi. The genes for the biosynthesis
           of TCP are part of a larger genetic element known as the
           TCP pathogenicity island.
          Length = 127

 Score = 23.9 bits (52), Expect = 7.6
 Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 1/45 (2%)

Query: 15  APALADPVAFAKDFIAGGVSAAVSKTAVAPIERVKLLLQVQHISK 59
           A A AD   F  D  A      V K+ +AP  +   L  + HI K
Sbjct: 71  AGAYADLTDFEVDMAAAATGVGVIKS-LAPGSKNLNLTNITHIEK 114


>gnl|CDD|234472 TIGR04105, FeFe_hydrog_B1, [FeFe] hydrogenase, group B1/B3.  See
           PMID:20395274 for descriptions of different groups.
          Length = 462

 Score = 24.1 bits (53), Expect = 8.4
 Identities = 10/19 (52%), Positives = 14/19 (73%), Gaps = 1/19 (5%)

Query: 20  DPVAFAKDF-IAGGVSAAV 37
           D  AF + F ++GGV+AAV
Sbjct: 384 DASAFGRGFAVSGGVAAAV 402


>gnl|CDD|236484 PRK09367, PRK09367, histidine ammonia-lyase; Provisional.
          Length = 500

 Score = 23.9 bits (53), Expect = 9.8
 Identities = 8/12 (66%), Positives = 10/12 (83%)

Query: 19  ADPVAFAKDFIA 30
            +PVAFA DF+A
Sbjct: 330 GEPVAFAADFLA 341


  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
   0.316    0.127    0.338 

Gapped
Lambda     K      H
   0.267   0.0709    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,548,970
Number of extensions: 262127
Number of successful extensions: 298
Number of sequences better than 10.0: 1
Number of HSP's gapped: 298
Number of HSP's successfully gapped: 19
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
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 (21.7 bits)
S2: 53 (24.2 bits)