RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2180
         (129 letters)



>gnl|CDD|238076 cd00131, PAX, Paired Box domain.
          Length = 128

 Score = 82.9 bits (205), Expect = 1e-21
 Identities = 33/41 (80%), Positives = 36/41 (87%)

Query: 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          G  G+NQLGGV+VNGRPLPDS RQ+IVELA SG RPCDISR
Sbjct: 1  GQGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISR 41


>gnl|CDD|128645 smart00351, PAX, Paired Box domain. 
          Length = 125

 Score = 82.0 bits (203), Expect = 3e-21
 Identities = 32/41 (78%), Positives = 36/41 (87%)

Query: 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          GH G+NQLGGV+VNGRPLPD  RQ+IVELA +G RPCDISR
Sbjct: 1  GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISR 41


>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain. 
          Length = 125

 Score = 80.2 bits (198), Expect = 1e-20
 Identities = 32/41 (78%), Positives = 35/41 (85%)

Query: 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          G   +NQLGGV+VNGRPLP+  RQKIVELAHSG RPCDISR
Sbjct: 1  GQGRVNQLGGVFVNGRPLPNHIRQKIVELAHSGVRPCDISR 41


>gnl|CDD|213264 cd03297, ABC_ModC_molybdenum_transporter, ATP-binding cassette
          domain of the molybdenum transport system.  ModC is an
          ABC-type transporter and the ATPase component of a
          molybdate transport system that also includes the
          periplasmic binding protein ModA and the membrane
          protein ModB. ABC transporters are a large family of
          proteins involved in the transport of a wide variety of
          different compounds, like sugars, ions, peptides and
          more complex organic molecules. The nucleotide binding
          domain shows the highest similarity between all members
          of the family. ABC transporters are a subset of
          nucleotide hydrolases that contain a signature motif,
          Q-loop, and H-loop/switch region, in addition to, the
          Walker A motif/P-loop and Walker B motif commonly found
          in a number of ATP- and GTP-binding and hydrolyzing
          proteins.
          Length = 214

 Score = 30.7 bits (70), Expect = 0.13
 Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 10/43 (23%)

Query: 6  ALFGCSAAGHSGINQL---------GGVYVNGRPLPDSTRQKI 39
           +FG S AG S + +          G + +NG  L DS R+KI
Sbjct: 27 GIFGASGAGKSTLLRCIAGLEKPDGGTIVLNGTVLFDS-RKKI 68


>gnl|CDD|177388 PHA02554, 13, neck protein; Provisional.
          Length = 311

 Score = 29.0 bits (65), Expect = 0.71
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 13  AGHSGINQLGGVYVNGRPLPDSTRQKIVEL 42
           A H G+   GGV ++GR L +  RQ+  +L
Sbjct: 266 AKHQGMQLPGGVTLDGRRLIEEARQEKEKL 295


>gnl|CDD|180645 PRK06649, PRK06649, V-type ATP synthase subunit K; Validated.
          Length = 143

 Score = 27.4 bits (61), Expect = 1.6
 Identities = 10/32 (31%), Positives = 16/32 (50%)

Query: 1  MAQSGALFGCSAAGHSGINQLGGVYVNGRPLP 32
          ++  G+  G  AAG + I      Y+ G+P P
Sbjct: 14 ISAIGSALGMGAAGMAAIGAWKRCYMQGKPAP 45


>gnl|CDD|238042 cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and
          similar prokaryotic, metal regulated homodimeric
          repressors. ARSR subfamily of helix-turn-helix
          bacterial transcription regulatory proteins (winged
          helix topology). Includes several proteins that appear
          to dissociate from DNA in the presence of metal ions.
          Length = 78

 Score = 26.5 bits (59), Expect = 2.0
 Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 1/28 (3%)

Query: 28 GRPLPDSTRQKIVE-LAHSGARPCDISR 54
           + L D TR +I+  L        +++ 
Sbjct: 1  LKALSDPTRLRILRLLLEGPLTVSELAE 28


>gnl|CDD|193235 pfam12759, HTH_Tnp_IS1, InsA C-terminal domain.  This short
          domain is found at the C-terminus of the InsA protein.
          This domain contains a helix-turn-helix domain.
          Length = 50

 Score = 26.0 bits (57), Expect = 2.0
 Identities = 8/21 (38%), Positives = 15/21 (71%)

Query: 35 TRQKIVELAHSGARPCDISRT 55
          T+++IV++A +GA     +RT
Sbjct: 14 TKEQIVDMAMNGAGCRYTART 34


>gnl|CDD|199207 cd08963, L-asparaginase_I, Type I (cytosolic) bacterial
           L-asparaginase.  Asparaginases (amidohydrolases, E.C.
           3.5.1.1) are enzymes that catalyze the hydrolysis of
           asparagine to aspartic acid and ammonia. In bacteria,
           there are two classes of amidohydrolases. This model
           represents type I L-asparaginases, which are highly
           specific for asparagine and localized in the cytosol.
           Type I L-asparaginase acts as a dimer. A conserved
           threonine residue is thought to supply the nucleophile
           hydroxy-group that attacks the amide bond. Many
           bacterial L-asparaginases have both L-asparagine and
           L-glutamine hydrolysis activities, to a different
           degree, and some of them are annotated as
           asparaginase/glutaminase. One example of an enzyme with
           no L-glutaminase activity is the type I L-asparaginase
           from Wolinella succinogenes.
          Length = 316

 Score = 27.5 bits (62), Expect = 2.0
 Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 1/48 (2%)

Query: 67  STSWAAFTSTGAPY-RTQRDRRSWNWRTLARDPVISRASCRSPTDVCR 113
           +TS+ AF S   P             R L  +P+ S        +V  
Sbjct: 159 TTSFDAFESINYPLLAEIGAGGLTLERLLQYEPLPSLFYPDLDPNVFL 206


>gnl|CDD|233249 TIGR01051, topA_bact, DNA topoisomerase I, bacterial.  This model
           describes DNA topoisomerase I among the members of
           bacteria. DNA topoisomerase I transiently cleaves one
           DNA strand and thus relaxes negatively supercoiled DNA
           during replication, transcription and recombination
           events [DNA metabolism, DNA replication, recombination,
           and repair].
          Length = 610

 Score = 27.3 bits (61), Expect = 2.7
 Identities = 11/44 (25%), Positives = 20/44 (45%)

Query: 22  GGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCSAVRRPATR 65
           G  Y+  +P    +++K  + AH   RP  + RT   ++    R
Sbjct: 321 GKEYLGPKPKRYKSKEKNAQEAHEAIRPTSVFRTPEELKDYLKR 364


>gnl|CDD|217041 pfam02448, L71, L71 family.  This family of insect proteins are
           each about 100 amino acids long and have 6 conserved
           cysteine residues. They all have a predicted signal
           peptide and are probably excreted. The function of the
           proteins is unknown.
          Length = 74

 Score = 25.5 bits (56), Expect = 3.4
 Identities = 10/35 (28%), Positives = 17/35 (48%), Gaps = 1/35 (2%)

Query: 84  RDRRSWNWRTLARDPVISRASCRSPTDVCRKFSAE 118
           R  R  NWR ++R   + +A+C      CR  + +
Sbjct: 33  RKVRGRNWRNVSR-CELQKANCLLTLRRCRTMNCK 66


>gnl|CDD|232834 TIGR00121, birA_ligase, birA, biotin-[acetyl-CoA-carboxylase]
          ligase region.  This model represents the
          biotin--acetyl-CoA-carboxylase ligase region of
          biotin--acetyl-CoA-carboxylase ligase. In Escherichia
          coli and some other species, this enzyme is part of a
          bifunction protein BirA that includes a small,
          N-terminal biotin operon repressor domain. Proteins
          identified by this model should not be called
          bifunctional unless they are also identified by
          birA_repr_reg (TIGR00122). The protein name suggests
          that this enzyme transfers biotin only to
          acetyl-CoA-carboxylase but it also transfers the biotin
          moiety to other proteins. The apparent orthologs among
          the eukaryotes are larger proteins that contain a
          single copy of this domain [Protein fate, Protein
          modification and repair].
          Length = 237

 Score = 26.6 bits (59), Expect = 3.8
 Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 3/35 (8%)

Query: 33 DSTRQKIVELAHSGARPCDISRTCSAVRRPATRGS 67
          DST Q  +ELA  G    D+     A  + A RG 
Sbjct: 9  DSTNQYALELAKEGKLKGDL---VVAEYQTAGRGR 40


>gnl|CDD|221227 pfam11795, DUF3322, Uncharacterized protein conserved in bacteria
           N-term (DUF3322).  This domain, found in various
           hypothetical bacterial proteins, has no known function.
           The family represents just the N-terminus.
          Length = 190

 Score = 26.2 bits (58), Expect = 5.2
 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 7/63 (11%)

Query: 51  DISRTCSAVRRPATRGSTSWAAFTSTGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD 110
            +S    AVR        +  A+     P   + + R+ N R L ++ + +R    S  +
Sbjct: 41  QLSEDFDAVRDW----IAALRAW---SRPGVYRVEWRTVNHRVLGKNELPARVVIDSLEE 93

Query: 111 VCR 113
             R
Sbjct: 94  ALR 96


>gnl|CDD|217758 pfam03843, Slp, Outer membrane lipoprotein Slp family. 
          Length = 160

 Score = 25.7 bits (57), Expect = 6.5
 Identities = 14/30 (46%), Positives = 15/30 (50%), Gaps = 1/30 (3%)

Query: 21 LGGVYVNGRPLPDSTRQKIVELA-HSGARP 49
           GGV V    L D TR +IV L   S  RP
Sbjct: 39 WGGVIVEVENLKDQTRLEIVSLPLDSSGRP 68


  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
   0.318    0.129    0.408 

Gapped
Lambda     K      H
   0.267   0.0723    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,304,393
Number of extensions: 517947
Number of successful extensions: 503
Number of sequences better than 10.0: 1
Number of HSP's gapped: 503
Number of HSP's successfully gapped: 22
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
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 (21.8 bits)
S2: 53 (24.2 bits)