RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6549
         (109 letters)



>gnl|CDD|152787 pfam12352, V-SNARE_C, Snare region anchored in the vesicle
          membrane C-terminus.  Within the SNARE proteins
          interactions in the C-terminal half of the SNARE helix
          are critical to the driving of membrane fusion; whereas
          interactions in the N-terminal half of the SNARE domain
          are important for promoting priming or docking of the
          vesicle pfam05008.
          Length = 66

 Score = 44.9 bits (107), Expect = 1e-07
 Identities = 22/66 (33%), Positives = 38/66 (57%)

Query: 14 QALVRTGESIVRSEQAALEAEAIGTGVISELGVQREALVRARDRLVDTDLHVSRSRRMIQ 73
          + L+R  + +  S + A E  +IG  ++ +L  QRE L RAR++L +TD  + +S   ++
Sbjct: 1  ERLLREHDRLKNSHRIADETISIGQAILEDLHSQRETLKRARNKLHNTDNRLGKSNSTLR 60

Query: 74 AIRRRV 79
           I RR 
Sbjct: 61 LINRRR 66


>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 = 26.4 bits (59), Expect = 1.1
 Identities = 13/50 (26%), Positives = 27/50 (54%)

Query: 21 ESIVRSEQAALEAEAIGTGVISELGVQREALVRARDRLVDTDLHVSRSRR 70
          E + + E++  E + I   + +EL  Q E L R  D + D D+++ ++ +
Sbjct: 12 EELEQLEKSIQELKQIFLDMGTELEEQGEQLDRIEDNVDDADVNLKKANK 61


>gnl|CDD|238940 cd01982, Chlide_reductase_Z, Chlide_reductase_Z : Z subunit of
           chlorophyllide (chlide) reductase (BchZ).  Chlide
           reductase participates in photosynthetic pigment
           synthesis playing a role in the conversion of
           chlorophylls(Chl) into bacteriochlorophylls (BChl).
           Chlide reductase catalyzes the reduction of the B-ring
           of the tetrapyrolle. Chlide reductase is a three subunit
           enzyme (subunits are designated BchX, BchY and BchZ).
           The similarity between these three subunits and the
           subunits for nitrogenase suggests that BchX serves as an
           electron donor for the BchY-BchY catalytic subunits.
          Length = 412

 Score = 27.5 bits (61), Expect = 1.6
 Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 3/51 (5%)

Query: 7   ETLRETNQALVRTGESIVRSEQAALEAEAIGTGVISELGVQREALVRARDR 57
             +  T   L  +G+ I+ S   + E+E IG+     L +Q+  +      
Sbjct: 73  GAVIRTIDKLDPSGKLILVS---SAESEMIGSDHTPMLTMQQPFVRFFIGE 120


>gnl|CDD|109709 pfam00662, Oxidored_q1_N, NADH-Ubiquinone oxidoreductase (complex
           I), chain 5 N-terminus.  This sub-family represents an
           amino terminal extension of pfam00361. Only
           NADH-Ubiquinone chain 5 and eubacterial chain L are in
           this family. This sub-family is part of complex I which
           catalyzes the transfer of two electrons from NADH to
           ubiquinone in a reaction that is associated with proton
           translocation across the membrane.
          Length = 62

 Score = 26.0 bits (58), Expect = 1.7
 Identities = 7/22 (31%), Positives = 13/22 (59%)

Query: 81  YNKLFLIMIIVIESMTLSVMLY 102
           ++ L LI + V+  ++  V LY
Sbjct: 21  FDSLSLIFLSVVLIVSWLVHLY 42


>gnl|CDD|185378 PRK15481, PRK15481, transcriptional regulatory protein PtsJ;
          Provisional.
          Length = 431

 Score = 26.9 bits (60), Expect = 2.3
 Identities = 13/29 (44%), Positives = 15/29 (51%)

Query: 42 SELGVQREALVRARDRLVDTDLHVSRSRR 70
          SELGV R  +  A  RLV   L  S+ R 
Sbjct: 37 SELGVNRNTVAAAYKRLVTAGLAQSQGRN 65


>gnl|CDD|237360 PRK13354, PRK13354, tyrosyl-tRNA synthetase; Provisional.
          Length = 410

 Score = 26.4 bits (59), Expect = 3.0
 Identities = 23/80 (28%), Positives = 30/80 (37%), Gaps = 13/80 (16%)

Query: 10  RETNQALVRTGESIVRSEQAALEAEAIGT-----GVISELGV----QREALVRARDRLVD 60
           R+  + L       V  E+AA EAE I        V     +             D LVD
Sbjct: 292 RDAKKVLAEEITKFVHGEEAAEEAEKIFKALFSGDVKPLKDIPTFEVSAETKNLVDLLVD 351

Query: 61  TDLHVSRS--RRMIQ--AIR 76
             L  S+   RR+IQ  AI+
Sbjct: 352 LGLEPSKREARRLIQNGAIK 371


>gnl|CDD|163426 TIGR03714, secA2, accessory Sec system translocase SecA2.  Members
           of this protein family are homologous to SecA and part
           of the accessory Sec system. This system, including both
           five core proteins for export and a variable number of
           proteins for glycosylation, operates in certain
           Gram-positive pathogens for the maturation and delivery
           of serine-rich glycoproteins such as the cell surface
           glycoprotein GspB in Streptococcus gordonii [Protein
           fate, Protein and peptide secretion and trafficking].
          Length = 762

 Score = 26.5 bits (59), Expect = 3.4
 Identities = 13/56 (23%), Positives = 19/56 (33%), Gaps = 3/56 (5%)

Query: 25  RSEQAALEAEAIGTGVISELGVQREALVRARDRLVDTDLHVSRSRRMIQAIRRRVF 80
            SE     A          L +QRE +   R+RL++           +  I   VF
Sbjct: 583 ASEDKGESAREQTNEFEESLSIQRENIYAERNRLIEGS---DFLDDDVDQIIDDVF 635


>gnl|CDD|177218 MTH00162, ND4L, NADH dehydrogenase subunit 4L; Provisional.
          Length = 89

 Score = 24.7 bits (55), Expect = 7.3
 Identities = 8/28 (28%), Positives = 16/28 (57%)

Query: 79  VFYNKLFLIMIIVIESMTLSVMLYLKIF 106
           +   K  L+M++ +E M LS+   L ++
Sbjct: 19  LSKRKHLLLMLLSLEFMVLSLFFLLFLY 46


>gnl|CDD|233912 TIGR02535, hyp_Hser_kinase, proposed homoserine kinase.  The genes
           in this family are largely adjacent to genes involved in
           the biosynthesis of threonine (aspartate kinase,
           homoserine dehydrogenase and threonine synthase) in
           genomes which are lacking any other known homoserine
           kinase, and in which the presence of a homoserine kinase
           would indicate a complete pathway for the biosynthesis
           of threonine. These genes are a member of the (now
           subfamily, formerly equivalog) TIGR00306 model
           describing the archaeal form of
           2,3-bisphosphoglycerate-independent phosphoglycerate
           mutase. All of these are members of a superfamily
           (pfam01676) of metalloenzyme also including
           phosphopentomutase alkaline phosphatases and sulfatases.
           The proposal that this family encodes a kinase is based
           on analogy to phosphomutases which are intramolecular
           phosphotransferases. A mutase active site could evolve
           to bring together homoserine and a phosphate donor such
           as phosphoenolpyruvate resulting in a kinase activity.
          Length = 396

 Score = 25.1 bits (55), Expect = 9.1
 Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 29  AALEAEAIGTGVISELGVQREALVRARDR-LVD-TDLHVS--RSRRMIQAIRRRVFYNKL 84
           A LEA +IG  +  +    R  LV   D  + D +  H+S   +  +I+ + + +   ++
Sbjct: 76  APLEAASIGVDLAPDEVAFRCNLVTVEDGKMKDFSAGHISSEEAATLIEDLNKELGSERV 135

Query: 85  F 85
            
Sbjct: 136 R 136


  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
   0.326    0.137    0.354 

Gapped
Lambda     K      H
   0.267   0.0788    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,671,320
Number of extensions: 523778
Number of successful extensions: 945
Number of sequences better than 10.0: 1
Number of HSP's gapped: 942
Number of HSP's successfully gapped: 64
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.1 bits)