RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9095
         (203 letters)



>gnl|CDD|224420 COG1503, eRF1, Peptide chain release factor 1 (eRF1) [Translation,
           ribosomal structure and biogenesis].
          Length = 411

 Score =  253 bits (647), Expect = 2e-83
 Identities = 84/194 (43%), Positives = 115/194 (59%)

Query: 10  VPPNGLVIYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALLADDNKFG 69
            P NGLV++ G ++   GK KKV +  EP +PINT LY CD+KF+ E L  +L D + +G
Sbjct: 83  TPENGLVLFVGDVLGGGGKTKKVTVVIEPPEPINTFLYRCDSKFYLEPLEEMLEDKDLYG 142

Query: 70  FIVMDGNGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAE 129
            IV+D   A  G L+G   EVL + T D+P KH  GGQSA RF RL  E  H + +KV E
Sbjct: 143 LIVLDRIEATIGLLKGKRIEVLKELTSDVPGKHRAGGQSARRFERLIEEAAHEFYKKVGE 202

Query: 130 VATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPRLQAKIIKLVDVSYGGENGFNQA 189
            A+  F+   K  + G+IL G    K E  + D     L+ K++ LVDVSY GE+G  + 
Sbjct: 203 AASEAFLPIAKKELKGIILGGPGPTKEEFVEGDYLHHELKKKVLGLVDVSYTGESGLREL 262

Query: 190 IELAAESLQNVLIV 203
           IE A ++L++V  V
Sbjct: 263 IEKAEDALKDVDYV 276


>gnl|CDD|234307 TIGR03676, aRF1/eRF1, peptide chain release factor 1, archaeal and
           eukaryotic forms.  Directs the termination of nascent
           peptide synthesis (translation) in response to the
           termination codons UAA, UAG and UGA. This model
           identifies both archaeal (aRF1) and eukaryotic (eRF1) of
           the protein. Also known as translation termination
           factor 1 [Protein synthesis, Translation factors].
          Length = 357

 Score =  240 bits (614), Expect = 3e-79
 Identities = 74/194 (38%), Positives = 107/194 (55%)

Query: 10  VPPNGLVIYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALLADDNKFG 69
            P NGLV++CG + T    EK      EP +PINT LY CD+KF+ E L  +L + + +G
Sbjct: 76  PPENGLVLFCGMVPTGGPGEKMETYVIEPPEPINTYLYRCDSKFYLEPLEEMLEEKDVYG 135

Query: 70  FIVMDGNGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAE 129
            IV+D   A  G L+G   EVL + T  +P KH  GGQSA RF RL     H + ++V E
Sbjct: 136 LIVLDRREATIGLLKGKRIEVLKELTSGVPGKHRAGGQSARRFERLIEIAAHEFYKRVGE 195

Query: 130 VATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPRLQAKIIKLVDVSYGGENGFNQA 189
            A   F+      + G+++ G    K E ++ D     L+ KII L DVSY GE+G  + 
Sbjct: 196 AANEAFLPLKDKKLKGILIGGPGPTKEEFAEGDYLHYELKKKIIGLFDVSYTGESGLREL 255

Query: 190 IELAAESLQNVLIV 203
           +E A + L+++  +
Sbjct: 256 VEKAEDLLKDLEYM 269


>gnl|CDD|235198 PRK04011, PRK04011, peptide chain release factor 1; Provisional.
          Length = 411

 Score =  171 bits (435), Expect = 1e-51
 Identities = 72/195 (36%), Positives = 106/195 (54%), Gaps = 1/195 (0%)

Query: 10  VPPNGLVIYCGTIVTE-EGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALLADDNKF 68
            P NGLVI+CG +     G E       EP +P+ T  Y CD++FHTE L  +L D   +
Sbjct: 83  PPENGLVIFCGAVPIGGPGTEDMETYVIEPPEPVPTFFYRCDSEFHTEPLEDMLEDKEVY 142

Query: 69  GFIVMDGNGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVA 128
           G IV+D   A  G L+G   EVL + T  +P KH +GGQSA RF RL  +  H + ++V 
Sbjct: 143 GLIVVDRREATIGLLKGKRIEVLKELTSFVPGKHRKGGQSARRFERLIEQAAHEFYKRVG 202

Query: 129 EVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPRLQAKIIKLVDVSYGGENGFNQ 188
           E A   F+   +  + G+++ G    K E  + D     L+ KI+ L DVSY GE+G  +
Sbjct: 203 EKANEAFLPLLEGKLKGILIGGPGPTKEEFLEGDYLHYELKKKILGLFDVSYTGESGLRE 262

Query: 189 AIELAAESLQNVLIV 203
            ++ A++ L+   +V
Sbjct: 263 LVDKASDLLKEQELV 277


>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 =  161 bits (409), Expect = 3e-51
 Identities = 70/136 (51%), Positives = 79/136 (58%), Gaps = 10/136 (7%)

Query: 67  KFGFIVMDGNGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRK 126
            +G IVMD   AL G L G   E+L K TV LP KHGRGGQSA RF     EKRH + RK
Sbjct: 1   DYGAIVMDEGEALIGLLTGYGIEILGKITVGLPGKHGRGGQSARRF----EEKRHEFYRK 56

Query: 127 VAEVATTLFITNDKPNIAGLILAGSADFKTELSQSDMFDPRLQA-KIIKLVDVSYGGENG 185
           VAE A   F   DK N+ G+ILAG    K E   SD  D RL   K I LVDVSYGGE G
Sbjct: 57  VAEAANQYF---DKDNVKGIILAGPGFTKNEFYDSDYLDYRLLKKKKIVLVDVSYGGEAG 113

Query: 186 FNQAIEL--AAESLQN 199
            N+ +E    A+ L +
Sbjct: 114 LNEVLERPAVADVLSD 129


>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 = 77.3 bits (191), Expect = 2e-18
 Identities = 25/58 (43%), Positives = 32/58 (55%), Gaps = 3/58 (5%)

Query: 9   LVPPNGLVIYCGTIVTEE---GKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALLA 63
             P NGL+ +CGTI+ E       K   +D EP +PI  S Y  D+KF TE L A+L 
Sbjct: 76  FDPENGLLRFCGTIIEENEDGKLGKYHTLDIEPPRPITISKYRWDSKFLTELLEAMLE 133


>gnl|CDD|183361 PRK11890, PRK11890, phosphate acetyltransferase; Provisional.
          Length = 312

 Score = 27.6 bits (62), Expect = 3.9
 Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 2/32 (6%)

Query: 115 LRMEKR--HNYVRKVAEVATTLFITNDKPNIA 144
           LR E+R  H +V  V      L IT+   NIA
Sbjct: 121 LRTERRISHVFVMDVPGYPKPLIITDAAVNIA 152


>gnl|CDD|239959 cd04586, CBS_pair_BON_assoc, This cd contains two tandem repeats of
           the cystathionine beta-synthase (CBS pair) domains
           associated with the BON (bacterial OsmY and nodulation
           domain) domain. BON is a putative phospholipid-binding
           domain found in a family of osmotic shock protection
           proteins. It is also found in some secretins and a group
           of potential haemolysins. Its likely function is
           attachment to phospholipid membranes. CBS is a small
           domain originally identified in cystathionine
           beta-synthase and subsequently found in a wide range of
           different proteins. CBS domains usually come in tandem
           repeats, which associate to form a so-called Bateman
           domain or a CBS pair which is reflected in this model.
           The interface between the two CBS domains forms a cleft
           that is a potential ligand binding site. The CBS pair
           coexists with a variety of other functional domains. It
           has been proposed that the CBS domain may play a
           regulatory role, although its exact function is unknown.
          Length = 135

 Score = 26.0 bits (58), Expect = 9.0
 Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 4/67 (5%)

Query: 72  VMDGNGALFGTL-QGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAEV 130
           V+D +G L G + +G   ++L +  +   ++  R          L      ++ RKVA+V
Sbjct: 30  VVDDDGRLVGIVSEG---DLLRRAELGTERRRARWLDLLAGAEELAAAFVRSHGRKVADV 86

Query: 131 ATTLFIT 137
            T   +T
Sbjct: 87  MTRPVVT 93


  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
   0.320    0.138    0.394 

Gapped
Lambda     K      H
   0.267   0.0748    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,307,855
Number of extensions: 963190
Number of successful extensions: 807
Number of sequences better than 10.0: 1
Number of HSP's gapped: 802
Number of HSP's successfully gapped: 9
Length of query: 203
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 111
Effective length of database: 6,857,034
Effective search space: 761130774
Effective search space used: 761130774
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 (21.8 bits)
S2: 57 (25.7 bits)