RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12115
         (154 letters)



>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of transcription
           factors; members include CAP (or cAMP receptor protein
           (CRP)), which binds cAMP, FNR (fumarate and nitrate
           reduction), which uses an iron-sulfur cluster to sense
           oxygen) and CooA, a heme containing CO sensor. In all
           cases binding of the effector leads to conformational
           changes and the ability to activate transcription.
           Cyclic nucleotide-binding domain similar to CAP are also
           present in cAMP- and cGMP-dependent protein kinases
           (cAPK and cGPK) and vertebrate cyclic nucleotide-gated
           ion-channels.  Cyclic nucleotide-monophosphate binding
           domain; proteins that bind cyclic nucleotides (cAMP or
           cGMP) share a structural domain of about 120 residues;
           the best studied is the prokaryotic catabolite gene
           activator, CAP, where such a domain is known to be
           composed of three alpha-helices and a distinctive
           eight-stranded, antiparallel beta-barrel structure;
           three conserved glycine residues are thought to be
           essential for maintenance of the structural integrity of
           the beta-barrel; CooA is a homodimeric transcription
           factor that belongs to CAP family; cAMP- and
           cGMP-dependent protein kinases (cAPK and cGPK) contain
           two tandem copies of the cyclic nucleotide-binding
           domain; cAPK's are composed of two different subunits, a
           catalytic chain and a regulatory chain, which contains
           both copies of the domain; cGPK's are single chain
           enzymes that include the two copies of the domain in
           their N-terminal section; also found in vertebrate
           cyclic nucleotide-gated ion-channels.
          Length = 115

 Score = 39.2 bits (92), Expect = 9e-05
 Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 2/55 (3%)

Query: 1   MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFA 55
           +  GD+FG+     N  G  +A VRALT  +L  + R     +L  Y   A    
Sbjct: 63  LGPGDLFGELALLGN--GPRSATVRALTDSELLVLPRSDFRRLLQEYPELARRLL 115


>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain. 
          Length = 91

 Score = 31.9 bits (73), Expect = 0.031
 Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 2/45 (4%)

Query: 1  MSKGDVFGDSFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLD 45
          +  GD FG+           +A V ALT  +L  I R+  LE+L+
Sbjct: 45 LGPGDFFGELALLGG--EPRSATVVALTDSELLVIPREDFLELLE 87


>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS.  [DNA
           metabolism, DNA replication, recombination, and repair].
          Length = 840

 Score = 29.0 bits (65), Expect = 1.1
 Identities = 38/156 (24%), Positives = 63/156 (40%), Gaps = 19/156 (12%)

Query: 15  NAVGQSAANVRALTYC------DLHTIKRDRLLEVLDFYQAFANSFARNLLLTYNLRHRK 68
             +G +AA    L Y        L  ++  RL E+ DF Q  A +  RNL LT NLR  K
Sbjct: 212 APLGLTAAG-CLLQYAKRTQRTALPHLQPVRLYELQDFMQLDAAT-RRNLELTENLRGGK 269

Query: 69  RDS----INLFVSSIISRIPLTYCDLHTIKRDRLLEVLDFYQAFANSFARNLLLTYNLR- 123
           +++    ++   +++ SR+   +       R+ L    D  +     F     L   L+ 
Sbjct: 270 QNTLFSVLDETKTAMGSRLLKRWLHRPLRDREVLEARQDTVEVLLRHFFLREGLRPLLKE 329

Query: 124 ----HRLVSNMTFITLTPK--TRLKNSMYIILEERG 153
                RL + +      P+   RL+ S+  + E R 
Sbjct: 330 VGDLERLAARVALGNARPRDLARLRTSLEQLPELRA 365


>gnl|CDD|239861 cd04396, RhoGAP_fSAC7_BAG7, RhoGAP_fSAC7_BAG7: RhoGAP
           (GTPase-activator protein [GAP] for Rho-like small
           GTPases) domain of fungal SAC7 and BAG7-like proteins.
           Both proteins are GTPase activating proteins of Rho1,
           but differ functionally in vivo: SAC7, but not BAG7, is
           involved in the control of Rho1-mediated activation of
           the PKC-MPK1 pathway. Small GTPases cluster into
           distinct families, and all act as molecular switches,
           active in their GTP-bound form but inactive when
           GDP-bound. The Rho family of GTPases activates effectors
           involved in a wide variety of developmental processes,
           including regulation of cytoskeleton formation, cell
           proliferation and the JNK signaling pathway. GTPases
           generally have a low intrinsic GTPase hydrolytic
           activity but there are family-specific groups of GAPs
           that enhance the rate of GTP hydrolysis by several
           orders of magnitude.
          Length = 225

 Score = 28.5 bits (64), Expect = 1.2
 Identities = 31/124 (25%), Positives = 47/124 (37%), Gaps = 11/124 (8%)

Query: 2   SKGDVFGDSF-WKDNAVGQSAANV--RALTYCDLHTIKRDRLLEVLDFYQAFANSFARNL 58
           S    +G SF W    V   AA+V  R L       +        LD Y+ F N   +  
Sbjct: 71  STPPDYGKSFDWDGYTV-HDAASVLRRYLNNLPEPLVP-------LDLYEEFRNPLRKRP 122

Query: 59  LLTYNLRHRKRDSINLFVSSIISRIPLTYCDLHTIKRDRLLEVLDFYQAFANSFARNLLL 118
            +   ++ R  + +N  +   I         L  + R  LL +LD    FA +  +NL+ 
Sbjct: 123 RILQYMKGRINEPLNTDIDQAIKEYRDLITRLPNLNRQLLLYLLDLLAVFARNSDKNLMT 182

Query: 119 TYNL 122
             NL
Sbjct: 183 ASNL 186


>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
           structure and biogenesis].
          Length = 178

 Score = 27.1 bits (61), Expect = 3.1
 Identities = 8/13 (61%), Positives = 9/13 (69%)

Query: 16  AVGQSAANVRALT 28
            VGQ AAN+RA  
Sbjct: 140 LVGQVAANIRAAR 152


>gnl|CDD|234384 TIGR03896, cyc_nuc_ocin, bacteriocin-type transport-associated
           protein.  Members of this protein family are
           uncharacterized and contain two copies of the cyclic
           nucleotide-binding domain pfam00027. Members are
           restricted to select cyanobacteria but are found
           regularly in association with a transport operon that,
           in turn, is associated with the production of putative
           bacteriocins. The models describing the transport operon
           are TIGR03794, TIGR03796, and TIGR03797.
          Length = 317

 Score = 26.4 bits (58), Expect = 6.9
 Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 5/72 (6%)

Query: 2   SKGDVFGD-SFWKDNAVGQSAANVRALTYCDLHTIKRDRLLEVLDFYQAFANSFARNLLL 60
            +G++ G+  F   N      A V+A+    L  I + +L   L     FA+ F R +  
Sbjct: 207 RRGEILGETPFL--NGSLPGTATVKAIENSVLLAIDKQQLAAKLQQDVGFASRFYRVIAS 264

Query: 61  TYNLRHRKRDSI 72
              L  R RD +
Sbjct: 265 L--LSQRSRDQV 274


  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
   0.328    0.139    0.408 

Gapped
Lambda     K      H
   0.267   0.0779    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,847,020
Number of extensions: 713302
Number of successful extensions: 732
Number of sequences better than 10.0: 1
Number of HSP's gapped: 731
Number of HSP's successfully gapped: 18
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
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 (21.8 bits)
S2: 55 (24.9 bits)