RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6196
         (146 letters)



>gnl|CDD|224454 COG1537, PelA, Predicted RNA-binding proteins [General function
           prediction only].
          Length = 352

 Score = 87.7 bits (218), Expect = 2e-21
 Identities = 29/96 (30%), Positives = 50/96 (52%)

Query: 41  GYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVA 100
                 G  ++  + V  G+YHT+++ +  + E+ K EW+   LER++ A    K  +VA
Sbjct: 76  NRLRIKGPIVEGPEEVVKGSYHTINVTIGTEIEIEKEEWNKDQLERLKEAVEASKRPEVA 135

Query: 101 AVMMQEGLANIMLITASMSLVRTKIETNIPRKRRGY 136
            V++ EG A I ++     ++  KI + IP KR G 
Sbjct: 136 IVVVDEGEAAIAIVRDYGIIILGKIRSGIPGKREGD 171



 Score = 32.3 bits (74), Expect = 0.065
 Identities = 8/23 (34%), Positives = 16/23 (69%)

Query: 1   MGAYHTLDLELNRKFELSKPEWD 23
            G+YHT+++ +  + E+ K EW+
Sbjct: 93  KGSYHTINVTIGTEIEIEKEEWN 115


>gnl|CDD|217574 pfam03463, eRF1_1, eRF1 domain 1.  The release factor eRF1
           terminates protein biosynthesis by recognising stop
           codons at the A site of the ribosome and stimulating
           peptidyl-tRNA bond hydrolysis at the peptidyl
           transferase centre. The crystal structure of human eRF1
           is known. The overall shape and dimensions of eRF1
           resemble a tRNA molecule with domains 1, 2, and 3 of
           eRF1 corresponding to the anticodon loop, aminoacyl
           acceptor stem, and T stem of a tRNA molecule,
           respectively. The position of the essential GGQ motif at
           an exposed tip of domain 2 suggests that the Gln residue
           coordinates a water molecule to mediate the hydrolytic
           activity at the peptidyl transferase centre. A conserved
           groove on domain 1, 80 A from the GGQ motif, is proposed
           to form the codon recognition site. This family also
           includes other proteins for which the precise molecular
           function is unknown. Many of them are from
           Archaebacteria. These proteins may also be involved in
           translation termination but this awaits experimental
           verification.
          Length = 133

 Score = 71.5 bits (176), Expect = 7e-17
 Identities = 24/58 (41%), Positives = 31/58 (53%)

Query: 36  FTPAVGYYYYCGRNIQENQYVKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNI 93
           F P  G   +CG  I+EN+  K+G YHTLD+E  R   +SK  WDS  L  +  A   
Sbjct: 76  FDPENGLLRFCGTIIEENEDGKLGKYHTLDIEPPRPITISKYRWDSKFLTELLEAMLE 133



 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 13/24 (54%), Positives = 16/24 (66%)

Query: 1   MGAYHTLDLELNRKFELSKPEWDS 24
           +G YHTLD+E  R   +SK  WDS
Sbjct: 98  LGKYHTLDIEPPRPITISKYRWDS 121


>gnl|CDD|129217 TIGR00111, pelota, mRNA surveillance protein pelota.  This model
           describes the Drosophila protein Pelota, the budding
           yeast protein DOM34 which it can replace, and a set of
           closely related archaeal proteins. Members contain a
           proposed RNA binding motif. The meiotic defect in pelota
           mutants may be a complex result of a protein translation
           defect, as suggested in yeast by ribosomal protein
           RPS30A being a multicopy suppressor and by an altered
           polyribosome profile in DOM34 mutants rescued by RPS30A.
           This family is homologous to a family of peptide chain
           release factors. Pelota is proposed to act in protein
           translation [Protein synthesis, Translation factors].
          Length = 351

 Score = 66.8 bits (163), Expect = 7e-14
 Identities = 27/79 (34%), Positives = 44/79 (55%)

Query: 56  VKMGAYHTLDLELNRKFELSKPEWDSIALERIEVACNIEKTADVAAVMMQEGLANIMLIT 115
           V +G+YHTL+++      + K  W    L+R+  A  I K    AAV+M+EG+A++ L+ 
Sbjct: 93  VPVGSYHTLEIKYVYPLSIIKQNWKKWQLKRLREAVEISKRPKTAAVVMEEGIAHVGLVR 152

Query: 116 ASMSLVRTKIETNIPRKRR 134
                   KIE ++P K+R
Sbjct: 153 QYSVEEIQKIEYHMPGKKR 171


>gnl|CDD|217575 pfam03464, eRF1_2, eRF1 domain 2.  The release factor eRF1
           terminates protein biosynthesis by recognising stop
           codons at the A site of the ribosome and stimulating
           peptidyl-tRNA bond hydrolysis at the peptidyl
           transferase centre. The crystal structure of human eRF1
           is known. The overall shape and dimensions of eRF1
           resemble a tRNA molecule with domains 1, 2, and 3 of
           eRF1 corresponding to the anticodon loop, aminoacyl
           acceptor stem, and T stem of a tRNA molecule,
           respectively. The position of the essential GGQ motif at
           an exposed tip of domain 2 suggests that the Gln residue
           coordinates a water molecule to mediate the hydrolytic
           activity at the peptidyl transferase centre. A conserved
           groove on domain 1, 80 A from the GGQ motif, is proposed
           to form the codon recognition site. This family also
           includes other proteins for which the precise molecular
           function is unknown. Many of them are from
           Archaebacteria. These proteins may also be involved in
           translation termination but this awaits experimental
           verification.
          Length = 129

 Score = 45.3 bits (108), Expect = 6e-07
 Identities = 13/37 (35%), Positives = 18/37 (48%)

Query: 98  DVAAVMMQEGLANIMLITASMSLVRTKIETNIPRKRR 134
           D  A++M EG A I L+T     +  KI   +P K  
Sbjct: 1   DYGAIVMDEGEALIGLLTGYGIEILGKITVGLPGKHG 37


>gnl|CDD|218583 pfam05420, BCSC_C, Cellulose synthase operon protein C C-terminus
           (BCSC_C).  This family contains the C-terminal regions
           of several bacterial cellulose synthase operon C (BCSC)
           proteins. BCSC is involved in cellulose synthesis
           although the exact function of this protein is unknown.
          Length = 339

 Score = 28.4 bits (64), Expect = 1.5
 Identities = 9/34 (26%), Positives = 21/34 (61%), Gaps = 2/34 (5%)

Query: 41  GYYYYCGRNIQENQYVKM--GAYHTLDLELNRKF 72
           GY+   G+N+++N  +++  G Y+ +  E +R+ 
Sbjct: 163 GYHVLTGKNVEDNTRLELMGGFYYRVINEDDRRL 196


>gnl|CDD|226664 COG4206, BtuB, Outer membrane cobalamin receptor protein [Coenzyme
           metabolism].
          Length = 608

 Score = 27.4 bits (61), Expect = 3.2
 Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 13/64 (20%)

Query: 3   AYHTLDLELNRKFELSKPEWDSLYTARIGLKSPFTPAVGYYYYCGRNIQENQYVKMGAYH 62
           A H +  EL+  F     ++D   T +          +G  Y    +      VK+G Y 
Sbjct: 513 ARHMVKYELDWAFY----DFDWGLTYQ---------YLGTRYDGDYSTYPANTVKLGGYS 559

Query: 63  TLDL 66
            LDL
Sbjct: 560 LLDL 563


>gnl|CDD|198453 cd10485, EphR_LBD_A7, Ligand Binding Domain of Ephrin type-A
           Receptor 7.  Ephrin receptors (EphRs) comprise the
           largest subfamily of receptor tyrosine kinases (RTKs).
           Class EphA receptors bind GPI-anchored ephrin-A ligands.
           There are ten vertebrate EphA receptors (EphA1-10),
           which display promiscuous interactions with six ephrin-A
           ligands. EphA7 has been implicated in various cancers,
           including prostate, gastic and colorectal cancers. EphRs
           contain a ligand binding domain and two fibronectin
           repeats extracellularly, a transmembrane segment, and a
           cytoplasmic tyrosine kinase domain. Binding of the
           ephrin ligand to EphR requires cell-cell contact since
           both are anchored to the plasma membrane. The resulting
           downstream signals occur bidirectionally in both
           EphR-expressing cells (forward signaling) and
           ephrin-expressing cells (reverse signaling).
          Length = 177

 Score = 26.9 bits (59), Expect = 3.5
 Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 5/21 (23%)

Query: 43  YYY-----CGRNIQENQYVKM 58
           YYY      GRNI+ENQYVK+
Sbjct: 97  YYYETDYDTGRNIRENQYVKI 117


>gnl|CDD|235502 PRK05560, PRK05560, DNA gyrase subunit A; Validated.
          Length = 805

 Score = 27.3 bits (62), Expect = 3.6
 Identities = 11/33 (33%), Positives = 17/33 (51%)

Query: 94  EKTADVAAVMMQEGLANIMLITASMSLVRTKIE 126
           EK   +   +  +    IMLIT S  L+RT++ 
Sbjct: 740 EKNGKLVGALPVDDDDEIMLITDSGKLIRTRVS 772


>gnl|CDD|233256 TIGR01063, gyrA, DNA gyrase, A subunit.  This model describes the
           common type II DNA topoisomerase (DNA gyrase). Two
           apparently independently arising families, one in the
           Proteobacteria and one in Gram-positive lineages, are
           both designated toposisomerase IV [DNA metabolism, DNA
           replication, recombination, and repair].
          Length = 800

 Score = 27.3 bits (61), Expect = 4.1
 Identities = 8/33 (24%), Positives = 18/33 (54%)

Query: 94  EKTADVAAVMMQEGLANIMLITASMSLVRTKIE 126
           ++   V   +  +    +MLIT++  L+RT ++
Sbjct: 737 DRNGQVVGAIAVDDDDELMLITSAGKLIRTSVQ 769


>gnl|CDD|236416 PRK09222, PRK09222, isocitrate dehydrogenase; Validated.
          Length = 482

 Score = 26.4 bits (59), Expect = 6.7
 Identities = 8/23 (34%), Positives = 13/23 (56%)

Query: 22 WDSLYTARIGLKSPFTPAVGYYY 44
          W+S+   ++ LK+P T   G  Y
Sbjct: 59 WESIRRTKVLLKAPITTPQGGGY 81


  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
   0.321    0.136    0.406 

Gapped
Lambda     K      H
   0.267   0.0736    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,301,006
Number of extensions: 632167
Number of successful extensions: 437
Number of sequences better than 10.0: 1
Number of HSP's gapped: 437
Number of HSP's successfully gapped: 20
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.6 bits)