RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13346
         (238 letters)



>gnl|CDD|238017 cd00060, FHA, Forkhead associated domain (FHA); found in eukaryotic
           and prokaryotic proteins. Putative nuclear signalling
           domain. FHA domains may bind phosphothreonine,
           phosphoserine and sometimes phosphotyrosine. In
           eukaryotes, many FHA domain-containing proteins localize
           to the nucleus, where they participate in establishing
           or maintaining cell cycle checkpoints, DNA repair, or
           transcriptional regulation. Members of the FHA family
           include: Dun1, Rad53,  Cds1, Mek1,
           KAPP(kinase-associated protein phosphatase),and Ki-67 (a
           human nuclear protein related to cell proliferation).
          Length = 102

 Score = 90.9 bits (226), Expect = 1e-23
 Identities = 34/99 (34%), Positives = 47/99 (47%), Gaps = 7/99 (7%)

Query: 119 KWRLYPFKNHQPLPIMYIHRQSAYIIGRNAKVSDILIRHCSCSNQHAVLQYRELSLNNTR 178
             RL            Y+     Y IGR++   DI++   S S +HAV++Y         
Sbjct: 1   VPRLVVLSGDASGRRYYLDPGGTYTIGRDSDNCDIVLDDPSVSRRHAVIRYDG------- 53

Query: 179 VVRPYLMDLKSMNGTFVNGMKIAPLTYVELFEGDVIEFG 217
                L+DL S NGTFVNG +++P   V L +GDVI  G
Sbjct: 54  DGGVVLIDLGSTNGTFVNGQRVSPGEPVRLRDGDVIRLG 92


>gnl|CDD|215951 pfam00498, FHA, FHA domain.  The FHA (Forkhead-associated) domain
           is a phosphopeptide binding motif.
          Length = 67

 Score = 69.2 bits (170), Expect = 8e-16
 Identities = 31/76 (40%), Positives = 40/76 (52%), Gaps = 9/76 (11%)

Query: 142 YIIGRNAKVSDILIRHCSCSNQHAVLQYRELSLNNTRVVRPYLMDLKSMNGTFVNGMKIA 201
             IGR+    DI++   S S +HA ++Y           R YL DL S NGTFVNG ++ 
Sbjct: 1   VTIGRSPD-CDIVLDDPSVSRRHAEIRYDGG-------GRFYLEDLGSTNGTFVNGQRLG 52

Query: 202 PLTYVELFEGDVIEFG 217
           P   V L +GDVI  G
Sbjct: 53  P-EPVRLRDGDVIRLG 67


>gnl|CDD|214578 smart00240, FHA, Forkhead associated domain.  Found in eukaryotic
           and prokaryotic proteins. Putative nuclear signalling
           domain.
          Length = 52

 Score = 56.8 bits (138), Expect = 2e-11
 Identities = 25/59 (42%), Positives = 33/59 (55%), Gaps = 7/59 (11%)

Query: 142 YIIGRNAKVSDILIRHCSCSNQHAVLQYRELSLNNTRVVRPYLMDLKSMNGTFVNGMKI 200
             IGR+++  DI +   S S +HAV+ Y        R    YL+DL S NGTFVNG +I
Sbjct: 1   VTIGRSSEDCDIQLDGPSISRRHAVIVYDG----GGRF---YLIDLGSTNGTFVNGKRI 52


>gnl|CDD|224630 COG1716, COG1716, FOG: FHA domain [Signal transduction mechanisms].
          Length = 191

 Score = 48.8 bits (116), Expect = 3e-07
 Identities = 29/87 (33%), Positives = 42/87 (48%), Gaps = 11/87 (12%)

Query: 136 IHRQSAYIIGRNAKVSDILIRHCSCSNQHAVLQYRELSLNNTRVVRPYLMDLKSMNGTFV 195
           +  +    IGR+   +DI++     S +HA L+      N       +L DL S NGT+V
Sbjct: 85  VLGEPVTTIGRD-PDNDIVLDDDVVSRRHAELRREG---NEV-----FLEDLGSTNGTYV 135

Query: 196 NGMKIAPLTYVELFEGDVIEFGLSTRE 222
           NG K+     V L +GDVI  G +  E
Sbjct: 136 NGEKVRQR--VLLQDGDVIRLGGTLAE 160


>gnl|CDD|113413 pfam04642, DUF601, Protein of unknown function, DUF601.  This
          family represents a conserved region found in several
          uncharacterized plant proteins.
          Length = 311

 Score = 30.4 bits (68), Expect = 0.81
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 3  TKQRASVPNQGKHQVCPKPSSRSYDGVPVMKPTDVSTEKTSRKRKHSDKTTRTPDDS--P 60
          ++Q+ S    GK+   P   SR+       K  D S     +KRK S+K  R+P  S  P
Sbjct: 27 SRQKPST-LAGKNPDAPTSESRTPSKATSSK--DPSKRYADKKRKQSEKDARSPPRSSRP 83

Query: 61 VTECHDSSPVKIR 73
           TE  D+ P + +
Sbjct: 84 RTEEKDAGPSQQK 96


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

 Score = 30.1 bits (68), Expect = 1.3
 Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 4/88 (4%)

Query: 15  HQVCPKPSSRSYDGVPVMKPTDVSTEKTSRKRKHSDKTTRTPDDSPVTECHDSSPVKIRR 74
           HQV P P+S+SY G+ V     +  E  +R R+     T+    S  +E           
Sbjct: 745 HQVLPGPASKSY-GLAVAALAGLPKEVIARARQI---LTQLEARSTESEAPQRKAQTSAP 800

Query: 75  EHASTFVASEDIAVKRKLDILKRSTLRP 102
           E  S F  +E   +  +L  L    L P
Sbjct: 801 EQISLFDEAETHPLLEELAKLDPDDLTP 828


>gnl|CDD|143179 cd04978, Ig4_L1-NrCAM_like, Fourth immunoglobulin (Ig)-like domain
           of L1, Ng-CAM (Neuron-glia CAM cell adhesion molecule),
           and NrCAM (Ng-CAM-related).  Ig4_L1-NrCAM_like: fourth
           immunoglobulin (Ig)-like domain of L1, Ng-CAM
           (Neuron-glia CAM cell adhesion molecule), and NrCAM
           (Ng-CAM-related). These proteins belong to the L1
           subfamily of cell adhesion molecules (CAMs) and are
           comprised of an extracellular region having six Ig-like
           domains and five fibronectin type III domains, a
           transmembrane region and an intracellular domain. These
           molecules are primarily expressed in the nervous system.
           L1 is associated with an X-linked recessive disorder,
           X-linked hydrocephalus, MASA syndrome, or spastic
           paraplegia type 1, that involves abnormalities of axonal
           growth.
          Length = 76

 Score = 27.7 bits (62), Expect = 1.4
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 4/48 (8%)

Query: 119 KWRL--YPFKNHQPLPIMYIHRQSAYIIGRNAKVSDILIRHCSCSNQH 164
            WRL   P +   P P   +   +  +I  N + +D  +  C+ SN H
Sbjct: 19  TWRLNGVPIEELPPDPRRRVDGGT--LILSNVQPNDTAVYQCNASNVH 64


>gnl|CDD|213299 cd05933, ACSBG_like, Bubblegum-like very long-chain fatty acid CoA
           synthetase (VL-FACS).  This family of very long-chain
           fatty acid CoA synthetase is named bubblegum because
           Drosophila melanogaster mutant bubblegum (BGM) has
           elevated levels of very-long-chain fatty acids (VLCFA)
           caused by a defective gene of this family. The human
           homolog (hsBG) has been characterized as a very long
           chain fatty acid CoA synthetase that functions
           specifically in the brain; hsBG may play a central role
           in brain VLCFA metabolism and myelinogenesis. VL-FACS is
           involved in the first reaction step of very long chain
           fatty acid degradation. It catalyzes the formation of
           fatty acyl-CoA in a two-step reaction: the formation of
           a fatty acyl-AMP molecule as an intermediate, and the
           formation of a fatty acyl-CoA. Free fatty acids must be
           "activated" to their CoA thioesters before participating
           in most catabolic and anabolic reactions.
          Length = 594

 Score = 28.5 bits (64), Expect = 3.3
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 1/47 (2%)

Query: 76  HASTFVASEDIAVKRKLDILKR-STLRPIVIYYEPKDAKLPSQYKWR 121
            A+  V      +++ L I  +   L+ I+ Y EP   K P+ Y W+
Sbjct: 80  EANILVVDNAKQLQKILAIQDQLPHLKAIIQYREPLKEKEPNLYSWK 126


>gnl|CDD|234178 TIGR03354, VI_FHA, type VI secretion system FHA domain protein.
           Members of this protein family are FHA
           (forkhead-associated) domain-containing proteins that
           are part of type VI secretion loci in a considerable
           number of bacteria, most of which are known pathogens.
           Species include Pseudomonas aeruginosa PAO1, Aeromonas
           hydrophila, Yersinia pestis, Burkholderia mallei, etc
           [Protein fate, Protein and peptide secretion and
           trafficking, Cellular processes, Pathogenesis].
          Length = 396

 Score = 28.5 bits (64), Expect = 3.5
 Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 13/60 (21%)

Query: 161 SNQHAVLQYRELSLNNTRVVRPYLMDLKSMNGTFVNGMKIAPLT---YVELFEGDVIEFG 217
           S +HA ++YR+            L DL S NG F+NG   +PL     V L +GD +  G
Sbjct: 46  SGRHARIRYRD--------GAYLLTDL-STNGVFLNG-SGSPLGRGNPVRLEQGDRLRLG 95


>gnl|CDD|178515 PLN02927, PLN02927, antheraxanthin epoxidase/zeaxanthin epoxidase.
          Length = 668

 Score = 27.8 bits (61), Expect = 5.7
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 13/70 (18%)

Query: 153 ILIRHCSCSNQHAVLQYRELSLNNTRVVRPYLMDLKSMNGTFVNG-----MKIAPLTYVE 207
           I+I     S  HA + Y++ +         +LMDL+S +GT+V        +  P     
Sbjct: 574 IVIPSSQVSKMHARVIYKDGAF--------FLMDLRSEHGTYVTDNEGRRYRATPNFPAR 625

Query: 208 LFEGDVIEFG 217
               D+IEFG
Sbjct: 626 FRSSDIIEFG 635


>gnl|CDD|219031 pfam06444, NADH_dehy_S2_C, NADH dehydrogenase subunit 2 C-terminus.
            This family consists of the C-terminal region specific
           to the eukaryotic NADH dehydrogenase subunit 2 protein
           and is found in conjunction with pfam00361.
          Length = 56

 Score = 25.2 bits (56), Expect = 6.2
 Identities = 11/22 (50%), Positives = 12/22 (54%)

Query: 115 PSQYKWRLYPFKNHQPLPIMYI 136
            S  KWRL P KN  PL I+  
Sbjct: 21  TSTTKWRLKPKKNTLPLAILST 42


>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
           replication, recombination, and repair].
          Length = 843

 Score = 27.2 bits (61), Expect = 9.5
 Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 1/37 (2%)

Query: 15  HQVCPKPSSRSYDGVPVMKPTDVSTEKTSRKRKHSDK 51
           ++V P  + +SY G+ V K   +  E   R R+   +
Sbjct: 760 YKVKPGIADKSY-GIHVAKLAGLPEEVIERAREILAE 795


  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    0.132    0.389 

Gapped
Lambda     K      H
   0.267   0.0799    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,586,908
Number of extensions: 1044515
Number of successful extensions: 690
Number of sequences better than 10.0: 1
Number of HSP's gapped: 686
Number of HSP's successfully gapped: 23
Length of query: 238
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 144
Effective length of database: 6,768,326
Effective search space: 974638944
Effective search space used: 974638944
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 (25.6 bits)