RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10606
         (128 letters)



>gnl|CDD|153134 cd01584, AcnA_Mitochondrial, Aconitase catalyzes the reversible
           isomerization of citrate and isocitrate as part of the
           TCA cycle.  Mitochondrial aconitase A catalytic domain.
           Aconitase (also known as aconitate hydratase and citrate
           hydro-lyase) catalyzes the reversible isomerization of
           citrate and isocitrate as part of the TCA cycle.
           Cis-aconitate is formed as an intermediary product
           during the course of the reaction. In eukaryotes two
           isozymes of aconitase are known to exist: one found in
           the mitochondrial matrix and the other found in the
           cytoplasm. This is the mitochondrial form. The
           mitochondrial product is coded by a nuclear gene. Most
           members of this subfamily are mitochondrial but there
           are some bacterial members.
          Length = 412

 Score = 29.3 bits (66), Expect = 0.46
 Identities = 20/58 (34%), Positives = 25/58 (43%), Gaps = 8/58 (13%)

Query: 53  IIQKIYSKRRVVRGCGYINEERDDCYRRTGTFDVDSTYCACKGDICNGSPSLGQSTSL 110
           +I K+     V  G G I E     Y   G   VDS  C   G ICN    +G +TS+
Sbjct: 153 VILKVAGILTVKGGTGAIVE-----YFGPG---VDSLSCTGMGTICNMGAEIGATTSV 202


>gnl|CDD|238372 cd00730, rubredoxin, Rubredoxin; nonheme iron binding domains
          containing a [Fe(SCys)4] center. Rubredoxins are small
          nonheme iron proteins. The iron atom is coordinated by
          four cysteine residues (Fe(S-Cys)4), but iron can also
          be replaced by cobalt, nickel or zinc. They are
          believed to be involved in electron transfer.
          Length = 50

 Score = 26.9 bits (60), Expect = 0.85
 Identities = 10/24 (41%), Positives = 11/24 (45%)

Query: 4  VCYQCNSAYDPRCGDPFDPYSLGT 27
           C  C   YDP  GDP +    GT
Sbjct: 3  ECRICGYIYDPAEGDPDEGIPPGT 26


>gnl|CDD|233362 TIGR01340, aconitase_mito, aconitate hydratase, mitochondrial.
           This model represents mitochondrial forms of the TCA
           cycle enzyme aconitate hydratase, also known as
           aconitase and citrate hydro-lyase [Energy metabolism,
           TCA cycle].
          Length = 745

 Score = 28.3 bits (63), Expect = 1.1
 Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 8/60 (13%)

Query: 51  RKIIQKIYSKRRVVRGCGYINEERDDCYRRTGTFDVDSTYCACKGDICNGSPSLGQSTSL 110
           + II K+     V  G GYI E     Y   G   V+S  C     ICN    +G +TS+
Sbjct: 208 KDIILKLAGLLTVRGGTGYIVE-----YFGPG---VESLSCTGMATICNMGAEIGATTSI 259


>gnl|CDD|130598 TIGR01535, glucan_glucosid, glucan 1,4-alpha-glucosidase.  Glucan
          1,4-alpha-glucosidase catalyzes the hydrolysis of
          terminal 1,4-linked alpha-D-glucose residues from
          non-reducing ends of polysaccharides, releasing a
          beta-D-glucose monomer. Some forms of this enzyme can
          hydrolyze terminal 1,6- and 1,3-alpha-D-glucosidic
          bonds in polysaccharides as well [Energy metabolism,
          Biosynthesis and degradation of polysaccharides].
          Length = 648

 Score = 27.5 bits (61), Expect = 2.6
 Identities = 5/26 (19%), Positives = 11/26 (42%)

Query: 63 VVRGCGYINEERDDCYRRTGTFDVDS 88
          V  G  ++++E  D   +   F   +
Sbjct: 32 VTDGKSFVSDETKDTTSKVEKFTDKA 57


>gnl|CDD|148049 pfam06210, DUF1003, Protein of unknown function (DUF1003).  This
           family consists of several hypothetical bacterial
           proteins of unknown function.
          Length = 108

 Score = 26.4 bits (59), Expect = 2.7
 Identities = 9/19 (47%), Positives = 13/19 (68%), Gaps = 4/19 (21%)

Query: 112 VTSLLAA----VVLLAQNR 126
           V SL AA    ++L++QNR
Sbjct: 41  VLSLQAAYQAPLILMSQNR 59


>gnl|CDD|184548 PRK14165, PRK14165, winged helix-turn-helix domain-containing
           protein/riboflavin kinase; Provisional.
          Length = 217

 Score = 25.8 bits (57), Expect = 6.8
 Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 1/30 (3%)

Query: 20  FDPYSLGTVNCSLLPIPENLLHKEYQTPVI 49
           F PY  GT+N  L      LL K  ++P I
Sbjct: 121 FIPY-PGTLNVKLDNSSSPLLRKLRESPGI 149


>gnl|CDD|189494 pfam00301, Rubredoxin, Rubredoxin. 
          Length = 47

 Score = 24.2 bits (53), Expect = 7.2
 Identities = 11/24 (45%), Positives = 12/24 (50%)

Query: 4  VCYQCNSAYDPRCGDPFDPYSLGT 27
          VC  C   YDP  GDP +    GT
Sbjct: 3  VCKVCGYVYDPAEGDPDNGIPPGT 26


>gnl|CDD|232836 TIGR00123, cbiM, cobalamin biosynthesis protein CbiM.  A cutoff of
           200 bits for trusted orthologs of cbiM is suggested.
           Scores lower than 200 but higher than 20 may be
           considered sufficient to call a protein cobalamin
           biosynthesis protein CbiM-related.The seed alignment for
           This model is a cluster of very closely related proteins
           from Methanobacterium thermoautotrophicum, Archaeoglobus
           fulgidus, Methanococcus jannaschii, and Salmonella
           typhimurium, each of which has greater than 50% identity
           to all the others. The ortholog from Salmonella is the
           source of the gene symbol cbiM for this set.In
           Methanobacterium thermoautotrophicum, Archaeoglobus
           fulgidus, and Methanococcus jannaschii, a second homolog
           of cbiM is also found. These cbiM-related proteins
           appear to represent a distinct but less well-conserved
           orthologous group. Still more distant homologs include
           sll0383 from Synechocystis sp. and HI1621 from
           Haemophilus influenzae; the latter protein, from a
           species that does not synthesize cobalamin, is the most
           divergent member of the group. The functions of and
           relationships among the set of proteins homologous to
           cbiM have not been determined [Biosynthesis of
           cofactors, prosthetic groups, and carriers, Heme,
           porphyrin, and cobalamin].
          Length = 214

 Score = 25.5 bits (56), Expect = 8.3
 Identities = 11/17 (64%), Positives = 14/17 (82%)

Query: 112 VTSLLAAVVLLAQNRLL 128
           VT++LAA+VLL Q  LL
Sbjct: 84  VTAVLAAIVLLFQALLL 100


>gnl|CDD|181384 PRK08319, PRK08319, cobalt transport protein CbiM; Validated.
          Length = 224

 Score = 25.6 bits (57), Expect = 8.7
 Identities = 10/17 (58%), Positives = 13/17 (76%)

Query: 112 VTSLLAAVVLLAQNRLL 128
           VT++L A+VLL Q  LL
Sbjct: 84  VTAVLGAIVLLFQALLL 100


  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
   0.323    0.140    0.441 

Gapped
Lambda     K      H
   0.267   0.0624    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,319,885
Number of extensions: 530664
Number of successful extensions: 388
Number of sequences better than 10.0: 1
Number of HSP's gapped: 387
Number of HSP's successfully gapped: 17
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.4 bits)