RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6235
         (76 letters)



>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain. 
          Length = 52

 Score = 50.2 bits (121), Expect = 2e-10
 Identities = 19/37 (51%), Positives = 22/37 (59%)

Query: 37 RREIANSNERRRMQSINAGFQSLRTLLPHHEGEKLSK 73
          RR+  N  ERRR   IN  F+ LR LLP    +KLSK
Sbjct: 1  RRKAHNERERRRRDRINDAFEELRELLPTPPNKKLSK 37


>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
          binding proteins that act as transcription factors;
          60-100 amino acids long. A DNA-binding basic region is
          followed by two alpha-helices separated by a variable
          loop region; HLH forms homo- and heterodimers,
          dimerization creates a parallel, left-handed, four
          helix bundle; the basic region N-terminal to the first
          amphipathic helix mediates high-affinity DNA-binding;
          there are several groups of HLH proteins: those
          (E12/E47) which bind specific hexanucleotide sequences
          such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
          those lacking the basic domain (Emc, Id) function as
          negative regulators since they fail to bind DNA, those
          (hairy, E(spl), deadpan) which repress transcription
          although they can bind specific hexanucleotide
          sequences such as N-box (5-CACGc/aG-3), those which
          have a COE domain (Collier/Olf-1/EBF) which is involved
          in both in dimerization and in DNA binding, and those
          which bind pentanucleotides ACGTG or GCGTG and have a
          PAS domain which allows the dimerization between PAS
          proteins, the binding of small molecules (e.g.,
          dioxin), and interactions with non-PAS proteins.
          Length = 60

 Score = 41.4 bits (98), Expect = 7e-07
 Identities = 20/38 (52%), Positives = 23/38 (60%), Gaps = 1/38 (2%)

Query: 37 RREIANSNERRRMQSINAGFQSLRTLLP-HHEGEKLSK 73
          RRE  N  ERRR + IN  F  LR+LLP     +KLSK
Sbjct: 4  RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSK 41


>gnl|CDD|197674 smart00353, HLH, helix loop helix domain. 
          Length = 53

 Score = 40.3 bits (95), Expect = 2e-06
 Identities = 17/33 (51%), Positives = 22/33 (66%), Gaps = 1/33 (3%)

Query: 42 NSNERRRMQSINAGFQSLRTLLP-HHEGEKLSK 73
          N+ ERRR + IN  F  LR+LLP   + +KLSK
Sbjct: 1  NARERRRRRKINEAFDELRSLLPTLPKNKKLSK 33


>gnl|CDD|223474 COG0397, COG0397, Uncharacterized conserved protein [Function
           unknown].
          Length = 488

 Score = 27.7 bits (62), Expect = 0.53
 Identities = 11/61 (18%), Positives = 18/61 (29%), Gaps = 5/61 (8%)

Query: 1   MTDFFFMKSNLGSENESPPR-----GPSHLLTPCTDKEKRIRREIANSNERRRMQSINAG 55
            T FF   S  G    +          +           R+  E  + + R  M+ +N  
Sbjct: 368 YTWFFRFLSWFGGWAAAEELALRFIDRAGFDAWEARYRLRLALEDFDPDRRIAMRLVNPA 427

Query: 56  F 56
           F
Sbjct: 428 F 428


>gnl|CDD|235962 PRK07201, PRK07201, short chain dehydrogenase; Provisional.
          Length = 657

 Score = 26.5 bits (59), Expect = 1.4
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 10/38 (26%)

Query: 36  IRREIANSNER-----RRMQSINAGFQSLR---TLLPH 65
           IRR + NS +R     R M  +N  F ++R    LLPH
Sbjct: 460 IRRSVENSTDRFHDYERTMA-VNY-FGAVRLILGLLPH 495


>gnl|CDD|223036 PHA03295, PHA03295, envelope glycoprotein H; Provisional.
          Length = 714

 Score = 25.8 bits (57), Expect = 2.0
 Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 8/49 (16%)

Query: 23  SHLLTPCTDKEKR--------IRREIANSNERRRMQSINAGFQSLRTLL 63
           +HL +P +   ++        I   + +S ERR + ++     S R L 
Sbjct: 426 THLFSPLSPFARQELYLLAEIIHSMLNHSRERRHIFALLTSLCSPRELY 474


>gnl|CDD|171585 PRK12566, PRK12566, glycine dehydrogenase; Provisional.
          Length = 954

 Score = 25.7 bits (56), Expect = 2.7
 Identities = 12/25 (48%), Positives = 15/25 (60%)

Query: 20  RGPSHLLTPCTDKEKRIRREIANSN 44
           RG + L      +E+ IRRE ANSN
Sbjct: 306 RGNTALRMALQTREQHIRREKANSN 330


>gnl|CDD|190527 pfam03110, SBP, SBP domain.  SBP domains (for SQUAMOSA-pROMOTER
          BINDING PROTEIN) are found in plant proteins. It is a
          sequence specific DNA-binding domain. Members of family
          probably function as transcription factors involved in
          the control of early flower development. The domain
          contains 10 conserved cysteine and histidine residues
          that probably are zinc ligands.
          Length = 79

 Score = 24.2 bits (53), Expect = 4.7
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 24 HLLTPCTDKEKRIRREIANSNERRR 48
          HLL+   + ++  RR +A  NERRR
Sbjct: 50 HLLSEFDEGKRSCRRRLAGHNERRR 74


>gnl|CDD|235432 PRK05367, PRK05367, glycine dehydrogenase; Provisional.
          Length = 954

 Score = 24.7 bits (55), Expect = 5.5
 Identities = 8/12 (66%), Positives = 9/12 (75%)

Query: 33  EKRIRREIANSN 44
           E+ IRRE A SN
Sbjct: 317 EQHIRREKATSN 328


  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
   0.316    0.131    0.381 

Gapped
Lambda     K      H
   0.267   0.0777    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,695,861
Number of extensions: 269251
Number of successful extensions: 255
Number of sequences better than 10.0: 1
Number of HSP's gapped: 255
Number of HSP's successfully gapped: 10
Length of query: 76
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 30
Effective length of database: 8,897,318
Effective search space: 266919540
Effective search space used: 266919540
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 (21.6 bits)
S2: 53 (24.1 bits)