RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10704
         (211 letters)



>gnl|CDD|214512 smart00091, PAS, PAS domain.  PAS motifs appear in archaea,
           eubacteria and eukarya. Probably the most surprising
           identification of a PAS domain was that in EAG-like
           K+-channels.
          Length = 67

 Score = 40.5 bits (95), Expect = 2e-05
 Identities = 15/55 (27%), Positives = 27/55 (49%)

Query: 148 SQTFLTKHSLDMKFTYADETMEDFLGFNPDIFIAKSVFDFHHAQDSFHIQNAFKN 202
               +    LD +  YA+   E+ LG++P+  I KS+ +  H +D   +Q A + 
Sbjct: 10  LPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQR 64



 Score = 28.5 bits (64), Expect = 0.45
 Identities = 9/23 (39%), Positives = 15/23 (65%)

Query: 4  DLMGQSIYEVTHPCDHSEVKSIL 26
          +L+G+S+ E+ HP D   V+  L
Sbjct: 40 ELIGKSLLELIHPEDRERVQEAL 62


>gnl|CDD|238075 cd00130, PAS, PAS domain; PAS motifs appear in archaea, eubacteria
           and eukarya. Probably the most surprising identification
           of a PAS domain was that in EAG-like K+-channels. PAS
           domains have been found to bind ligands, and to act as
           sensors for light and oxygen in signal transduction.
          Length = 103

 Score = 40.3 bits (94), Expect = 6e-05
 Identities = 15/53 (28%), Positives = 26/53 (49%)

Query: 150 TFLTKHSLDMKFTYADETMEDFLGFNPDIFIAKSVFDFHHAQDSFHIQNAFKN 202
             +    LD +  YA+   E  LG++P+  I KS+ D  H +D   ++   +N
Sbjct: 3   DGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLEN 55



 Score = 30.7 bits (69), Expect = 0.19
 Identities = 11/42 (26%), Positives = 21/42 (50%)

Query: 4  DLMGQSIYEVTHPCDHSEVKSILSANHTEDIRAQRSVFIRLK 45
          +L+G+S+ ++ HP D  E++  L    +        V +R K
Sbjct: 31 ELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRK 72


>gnl|CDD|216228 pfam00989, PAS, PAS fold.  The PAS fold corresponds to the
          structural domain that has previously been defined as
          PAS and PAC motifs. The PAS fold appears in archaea,
          eubacteria and eukarya.
          Length = 113

 Score = 33.2 bits (76), Expect = 0.031
 Identities = 8/50 (16%), Positives = 19/50 (38%), Gaps = 4/50 (8%)

Query: 4  DLMGQSIYEVTHPCDHSEVKSILSANHTEDIRAQRSVFIRLKCTLTSKGR 53
          +++G+S+ ++    D +EV  +L     + +                 GR
Sbjct: 40 EVIGKSLLDLIPEDDDAEVAELL----RQALLQGEESRGFEVSFRVPDGR 85


>gnl|CDD|130302 TIGR01235, pyruv_carbox, pyruvate carboxylase.  This enzyme plays a
           role in gluconeogensis but not glycolysis [Energy
           metabolism, Glycolysis/gluconeogenesis].
          Length = 1143

 Score = 31.3 bits (71), Expect = 0.42
 Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 15/61 (24%)

Query: 71  LVQNQTPASNGSTLMEPQDNIENQSDNTRRGSAIQDKDDSEPEEEVGEKRRVVTE-PSHC 129
           +VQ Q   ++G++L  PQ  + NQ D    G AIQ               RV TE P++ 
Sbjct: 308 IVQAQIHIADGASLPTPQLGVPNQEDIRTNGYAIQC--------------RVTTEDPANN 353

Query: 130 F 130
           F
Sbjct: 354 F 354


>gnl|CDD|222120 pfam13426, PAS_9, PAS domain. 
          Length = 101

 Score = 28.5 bits (64), Expect = 0.96
 Identities = 9/47 (19%), Positives = 17/47 (36%)

Query: 156 SLDMKFTYADETMEDFLGFNPDIFIAKSVFDFHHAQDSFHIQNAFKN 202
             D +  YA++     LG+  +  + KS+ D     D        + 
Sbjct: 5   DPDGRIVYANDAALRLLGYTREELLGKSIRDLFGPGDDEEAVARLRE 51


>gnl|CDD|237263 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
          Length = 1146

 Score = 29.7 bits (68), Expect = 1.1
 Identities = 14/35 (40%), Positives = 21/35 (60%)

Query: 71  LVQNQTPASNGSTLMEPQDNIENQSDNTRRGSAIQ 105
           +VQ+Q   + G+TL + +  I +Q D   RG AIQ
Sbjct: 312 IVQSQILIAEGATLHDLEIGIPSQEDIRLRGYAIQ 346


>gnl|CDD|223968 COG1038, PycA, Pyruvate carboxylase [Energy production and
           conversion].
          Length = 1149

 Score = 28.5 bits (64), Expect = 2.9
 Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 15/61 (24%)

Query: 71  LVQNQTPASNGSTLMEPQDNIENQSDNTRRGSAIQDKDDSEPEEEVGEKRRVVTE-PSHC 129
           +V+ Q   + G+TL  P+  +  Q D    G AIQ               R+ TE P + 
Sbjct: 314 IVKAQIHIAAGATLHTPELGLPQQKDIRTHGYAIQC--------------RITTEDPENG 359

Query: 130 F 130
           F
Sbjct: 360 F 360


>gnl|CDD|107202 cd00640, Trp-synth-beta_II, Tryptophan synthase beta superfamily
           (fold type II); this family of pyridoxal phosphate
           (PLP)-dependent enzymes catalyzes beta-replacement and
           beta-elimination reactions. This CD corresponds to
           aminocyclopropane-1-carboxylate deaminase (ACCD),
           tryptophan synthase beta chain (Trp-synth_B),
           cystathionine beta-synthase (CBS), O-acetylserine
           sulfhydrylase (CS), serine dehydratase (Ser-dehyd),
           threonine dehydratase (Thr-dehyd), diaminopropionate
           ammonia lyase (DAL), and threonine synthase (Thr-synth).
           ACCD catalyzes the conversion of
           1-aminocyclopropane-1-carboxylate  to alpha-ketobutyrate
           and ammonia. Tryptophan synthase folds into a tetramer,
           where the beta chain is the catalytic PLP-binding
           subunit and catalyzes the formation of L-tryptophan from
           indole and L-serine. CBS is a tetrameric hemeprotein
           that catalyzes condensation of serine and homocysteine
           to cystathionine. CS is a homodimer that catalyzes the
           formation of L-cysteine from O-acetyl-L-serine.
           Ser-dehyd catalyzes the conversion of L- or D-serine  to
           pyruvate and ammonia. Thr-dehyd is active as a homodimer
           and catalyzes the conversion of L-threonine to
           2-oxobutanoate and ammonia. DAL is also a homodimer and
           catalyzes the alpha, beta-elimination reaction of both
           L- and D-alpha, beta-diaminopropionate to form pyruvate
           and ammonia. Thr-synth catalyzes the formation of
           threonine and inorganic phosphate from
           O-phosphohomoserine.
          Length = 244

 Score = 27.1 bits (61), Expect = 5.9
 Identities = 6/20 (30%), Positives = 8/20 (40%)

Query: 162 TYADETMEDFLGFNPDIFIA 181
           T   E +E   G  PD  + 
Sbjct: 140 TIGLEILEQLGGQKPDAVVV 159


>gnl|CDD|235828 PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase;
           Validated.
          Length = 953

 Score = 27.2 bits (61), Expect = 8.8
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 12/47 (25%)

Query: 143 YDVPLSQTFLTKHSLDMKFTYADETMEDFLGF--NPDIFIAKSVFDF 187
           Y VPL + +++K S +M+F  A        G   +PDI IAKS+ D+
Sbjct: 797 YGVPL-EVYVSKFS-NMRFEPA--------GMTDDPDIRIAKSIMDY 833


  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
   0.317    0.131    0.389 

Gapped
Lambda     K      H
   0.267   0.0686    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,136,017
Number of extensions: 894436
Number of successful extensions: 663
Number of sequences better than 10.0: 1
Number of HSP's gapped: 663
Number of HSP's successfully gapped: 14
Length of query: 211
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 118
Effective length of database: 6,812,680
Effective search space: 803896240
Effective search space used: 803896240
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: 57 (25.8 bits)