RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy7328
         (159 letters)



>gnl|CDD|203323 pfam05739, SNARE, SNARE domain.  Most if not all vesicular membrane
           fusion events in eukaryotic cells are believed to be
           mediated by a conserved fusion machinery, the SNARE
           [soluble N-ethylmaleimide-sensitive factor (NSF)
           attachment protein (SNAP) receptors] machinery. The
           SNARE domain is thought to act as a protein-protein
           interaction module in the assembly of a SNARE protein
           complex.
          Length = 62

 Score = 46.0 bits (110), Expect = 1e-07
 Identities = 16/54 (29%), Positives = 30/54 (55%)

Query: 77  QDQGLEALSKVISRQKNIALTISNEVDVQNDLVDDITERMDHTNVSIQRETNQV 130
           +D+ LE L   I   K + L +  EV+ Q +L+D I + +D+T   ++R   ++
Sbjct: 1   RDEALEELESSIGELKQLFLDMGEEVEEQGELLDRIDDNVDNTQSRVERANKRL 54


>gnl|CDD|197699 smart00397, t_SNARE, Helical region found in SNAREs.  All
           alpha-helical motifs that form twisted and parallel
           four-helix bundles in target soluble
           N-ethylmaleimide-sensitive factor (NSF) attachment
           protein (SNAP) receptor proteins. This motif found in
           "Q-SNAREs".
          Length = 66

 Score = 44.9 bits (107), Expect = 4e-07
 Identities = 16/66 (24%), Positives = 33/66 (50%)

Query: 68  EQQQMMIAAQDQGLEALSKVISRQKNIALTISNEVDVQNDLVDDITERMDHTNVSIQRET 127
           +Q       +D+ LE L K I   K I L +  E++ Q + +D I + +D  +V++++  
Sbjct: 1   QQALAREEERDEELEQLEKSIQELKQIFLDMGTELEEQGEQLDRIEDNVDDADVNLKKAN 60

Query: 128 NQVTSI 133
            ++   
Sbjct: 61  KRLKKA 66


>gnl|CDD|238115 cd00193, t_SNARE, Soluble NSF (N-ethylmaleimide-sensitive fusion
           protein)-Attachment protein (SNAP) REceptor domain;
           these alpha-helical motifs form twisted and parallel
           heterotetrameric helix bundles; the core complex
           contains one helix from a protein that is anchored in
           the vesicle membrane (synaptobrevin), one helix from a
           protein of the target membrane (syntaxin), and two
           helices from another protein anchored in the target
           membrane (SNAP-25); their interaction forms a core which
           is composed of a polar zero layer, a flanking
           leucine-zipper layer acts as a water tight shield to
           isolate ionic interactions in the zero layer from the
           surrounding solvent.
          Length = 60

 Score = 43.6 bits (104), Expect = 8e-07
 Identities = 17/57 (29%), Positives = 32/57 (56%)

Query: 77  QDQGLEALSKVISRQKNIALTISNEVDVQNDLVDDITERMDHTNVSIQRETNQVTSI 133
           +D+ LE L   I   K I L +  EV+ Q +L+D I + +D+ +V+++R   ++   
Sbjct: 4   RDEELEQLEASIGELKQIFLDLGTEVEEQGELLDRIEDNVDNADVNVKRANKRLKKA 60


>gnl|CDD|221952 pfam13166, AAA_13, AAA domain.  This family of domains contain a
           P-loop motif that is characteristic of the AAA
           superfamily. Many of the proteins in this family are
           conjugative transfer proteins. This family includes the
           PrrC protein that is thought to be the active component
           of the anticodon nuclease.
          Length = 713

 Score = 29.2 bits (66), Expect = 0.86
 Identities = 24/131 (18%), Positives = 49/131 (37%), Gaps = 29/131 (22%)

Query: 8   QRLLEQLQSSSVKITNMYNNRPSYSAQRNELFADVGTTGWGDDASDEESPLLGANIADVR 67
           + L+++ +S   K      +      + +E   DV                L A +  + 
Sbjct: 288 EELIDKYESHIEKALEELESILDTEKENSEFKLDVE--------------ELKALLEALE 333

Query: 68  EQQQMMIAAQDQGLEALSKVI-SRQKNIALTISNEVDVQNDLVDDITERMDHTNVSIQRE 126
           E            LE   + +  + K+ + +I  E++   DL++ I + +D  N  I RE
Sbjct: 334 EI-----------LEKNLQKLEEKLKDPSTSI--ELESITDLIESINDIIDAINELI-RE 379

Query: 127 TNQVTSILTQD 137
            N+    L ++
Sbjct: 380 HNEKIDNLKKE 390


>gnl|CDD|227635 COG5325, COG5325, t-SNARE complex subunit, syntaxin [Intracellular
           trafficking and secretion].
          Length = 283

 Score = 28.3 bits (63), Expect = 1.6
 Identities = 18/89 (20%), Positives = 42/89 (47%)

Query: 68  EQQQMMIAAQDQGLEALSKVISRQKNIALTISNEVDVQNDLVDDITERMDHTNVSIQRET 127
           E QQ++I  +D+ ++ L++ I     I   + + V  Q +LVD I   +++T+ +++   
Sbjct: 184 EYQQILITERDEEIKNLARGIYELNEIFRDLGSLVGEQGELVDRIDFNIENTSDNLKNAN 243

Query: 128 NQVTSILTQDATCGYWVVIIVLFIANVLV 156
            ++                ++L +  VL+
Sbjct: 244 KELEKAPAHQRRTKKCRFYLLLILLVVLL 272


>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 944

 Score = 27.8 bits (62), Expect = 3.0
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 4/67 (5%)

Query: 48  GDDASDEESPLLGANIADVREQQQMMIAAQDQGLEALSKVISRQKNIALTISNEVDVQND 107
            + A D+ES LL A  A   EQ  ++  AQ QG EA S  +    +      +    Q+ 
Sbjct: 442 VEQALDDESELLAALNA---EQAVILSQAQSQGFEA-SSSLDADNSAVPEQIDSTAEQSV 497

Query: 108 LVDDITE 114
           +   +T+
Sbjct: 498 VNPSVTD 504


>gnl|CDD|129249 TIGR00144, beta_RFAP_syn, beta-RFAP synthase.  This protein family
           contains several archaeal examples of
           beta-ribofuranosylaminobenzene 5-prime-phosphate
           synthase (beta-RFAP synthase), an enzyme involved in
           methanopterin biosynthesis. In some species, two members
           of this family are found. It is unclear whether both act
           as beta-RFAP synthase. This family is related to the
           GHMP kinases (Galactokinase, Homoserine kinase,
           Mevalonate kinase, Phosphomevalonate kinase). Members
           are found so far only in the Archaea and in
           Methylobacterium extorquens [Unknown function, Enzymes
           of unknown specificity].
          Length = 324

 Score = 26.8 bits (59), Expect = 5.4
 Identities = 10/47 (21%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 71  QMMIAAQDQGLEALSKVISRQKNIALTISNEVDVQNDLVDDITERMD 117
           +MM A  +  L+A  + ++  + +      E ++Q+ L+  I + M 
Sbjct: 224 KMMPAVVEGDLDAFGESVNEIQGLGFK-KIERELQDPLIKRIIDSMI 269


>gnl|CDD|198079 smart01011, AMP_N, Aminopeptidase P, N-terminal domain.  This
          domain is structurally very similar to the creatinase
          N-terminal domain. However, little or no sequence
          similarity exists between the two families.
          Length = 135

 Score = 25.7 bits (57), Expect = 8.7
 Identities = 7/15 (46%), Positives = 9/15 (60%)

Query: 5  ERRQRLLEQLQSSSV 19
           RR+RL  +L   SV
Sbjct: 8  ARRRRLAAKLFPGSV 22


  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
   0.315    0.128    0.346 

Gapped
Lambda     K      H
   0.267   0.0766    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,657,956
Number of extensions: 671162
Number of successful extensions: 823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 823
Number of HSP's successfully gapped: 22
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
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: 55 (24.9 bits)