RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13149
         (89 letters)



>gnl|CDD|189476 pfam00261, Tropomyosin, Tropomyosin. 
          Length = 237

 Score = 41.5 bits (98), Expect = 1e-05
 Identities = 17/25 (68%), Positives = 22/25 (88%)

Query: 1   MDALENQLKEARFLAEEADKKYDEV 25
           M+ LE QLKEA+ +AEEAD+KY+EV
Sbjct: 94  MEQLEAQLKEAKEIAEEADRKYEEV 118



 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 17/26 (65%), Positives = 22/26 (84%)

Query: 45  MDALENQLKEARFLAEEADKKYDETA 70
           M+ LE QLKEA+ +AEEAD+KY+E A
Sbjct: 94  MEQLEAQLKEAKEIAEEADRKYEEVA 119


>gnl|CDD|240314 PTZ00208, PTZ00208, 65 kDa invariant surface glycoprotein;
           Provisional.
          Length = 436

 Score = 28.0 bits (62), Expect = 0.51
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 2   DALENQLKEARFLAEEADKKYDEV 25
           D +  QL EA+   EEA+K + EV
Sbjct: 115 DGIAKQLPEAKKAGEEAEKLHQEV 138



 Score = 26.5 bits (58), Expect = 2.2
 Identities = 10/23 (43%), Positives = 14/23 (60%)

Query: 46  DALENQLKEARFLAEEADKKYDE 68
           D +  QL EA+   EEA+K + E
Sbjct: 115 DGIAKQLPEAKKAGEEAEKLHQE 137


>gnl|CDD|200530 cd11269, Sema_6D, The Sema domain, a protein interacting module, of
           semaphorin 6D (Sema6D).  Sema6D is expressed
           predominantly in the nervous system during embryogenesis
           and it uses Plexin-A1 as a receptor. It displays
           repellent activity for dorsal root ganglion axons.
           Sema6D also acts as a regulator of late phase primary
           immune responses. In addition, Sema6D is overexpressed
           in gastric carcinoma, indicating that it may have an
           important role in the occurrence and development of the
           cancer. Sema6D is a member of the class 6 semaphorin
           family of proteins, which are membrane associated
           semaphorins. Semaphorins are regulatory molecules
           involved in the development of the nervous system and in
           axonal guidance. They also play important roles in other
           biological processes, such as angiogenesis, immune
           regulation, respiration systems and cancer. The Sema
           domain is located at the N-terminus and contains four
           disulfide bonds formed by eight conserved cysteine
           residues. It serves as a receptor-recognition and
           -binding module.
          Length = 465

 Score = 26.5 bits (58), Expect = 1.8
 Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 2/37 (5%)

Query: 23  DEVIFVCGNRERRFFPIQKYFFMDALENQLKEARFLA 59
           DE++FVCG     F P+ +Y+ +  LE   +E   LA
Sbjct: 82  DEMVFVCGTNA--FNPMCRYYRLSTLEYDGEEISGLA 116


>gnl|CDD|233466 TIGR01553, formate-DH-alph, formate dehydrogenase, alpha subunit,
           proteobacterial-type.  This model describes a subset of
           formate dehydrogenase alpha chains found mainly in
           proteobacteria but also in Aquifex. The alpha chain
           contains domains for molybdopterin dinucleotide binding
           and molybdopterin oxidoreductase (pfam01568 and
           pfam00384, respectively). The holo-enzyme also contains
           beta and gamma subunits of 32 and 20 kDa. The enzyme
           catalyzes the oxidation of formate (produced from
           pyruvate during anaerobic growth) to carbon dioxide with
           the concomitant release of two electrons and two
           protons. The electrons are utilized mainly in the
           nitrate respiration by nitrate reductase. In E. coli and
           Salmonella, there are two forms of the formate
           dehydrogenase, one induced by nitrate which is strictly
           anaerobic (fdn), and one incuced during the transition
           from aerobic to anaerobic growth (fdo). This subunit is
           one of only three proteins in E. coli which contain
           selenocysteine. This model is well-defined, with a
           large, unpopulated trusted/noise gap [Energy metabolism,
           Anaerobic, Energy metabolism, Electron transport].
          Length = 1009

 Score = 26.0 bits (57), Expect = 3.1
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 19  DKKYDEVIFVCGNRERRFFPIQKYFFMDALENQLKEARFLAEEADKKYDETAGVKGLFSP 78
           D K  ++I V G       PI    F  A+  + K A+ +    D +++ TA V  L++P
Sbjct: 218 DIKNSDLILVMGGNPAENHPIG---FKWAIRAKKKGAKIIH--IDPRFNRTATVADLYAP 272

Query: 79  IRA 81
           IR+
Sbjct: 273 IRS 275


>gnl|CDD|213394 cd12151, F1-ATPase_gamma, mitochondrial ATP synthase gamma subunit.
            The F-ATPase is found in bacterial plasma membranes,
           mitochondrial inner membranes and in chloroplast
           thylakoid membranes. It has also been found in the
           archaea Methanosarcina barkeri. It uses a proton
           gradient to drive ATP synthesis and hydrolyzes ATP to
           build the proton gradient. The extrinisic membrane
           domain of F-ATPases is composed of alpha, beta, gamma,
           delta, and epsilon (not present in bacteria) subunits
           with a stoichiometry of 3:3:1:1:1. Alpha and beta
           subunit form the globular catalytic moiety, a hexameric
           ring of alternating subunits. Gamma, delta and epsilon
           subunits form a stalk, connecting F1 to F0, the integral
           membrane proton translocating domain.
          Length = 282

 Score = 25.6 bits (57), Expect = 4.1
 Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 6/69 (8%)

Query: 5   ENQLKEARFLAEEADKKYDEVIFVCGNR-----ERRFFPIQKYFFMDALENQLKEARFLA 59
            N +K A  L +EAD K  ++I V G +     +RR + I   F     +    EA  + 
Sbjct: 92  SNIIKAAEELIKEADGKEVKLIVV-GKKGRDYLKRRGYNIALPFSDIGDDPTYFEAASII 150

Query: 60  EEADKKYDE 68
           EE    +  
Sbjct: 151 EELILDFLN 159


>gnl|CDD|218630 pfam05546, She9_MDM33, She9 / Mdm33 family.  Members of this
          family are mitochondrial inner membrane proteins with a
          role in inner mitochondrial membrane organisation and
          biogenesis.
          Length = 208

 Score = 25.4 bits (56), Expect = 4.5
 Identities = 11/25 (44%), Positives = 14/25 (56%)

Query: 2  DALENQLKEARFLAEEADKKYDEVI 26
          + LE QL+ A+    EA K Y E I
Sbjct: 42 EELETQLRAAKEEVREAKKAYSEAI 66


>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family. 
          Length = 168

 Score = 24.9 bits (55), Expect = 5.6
 Identities = 9/19 (47%), Positives = 9/19 (47%)

Query: 10  EARFLAEEADKKYDEVIFV 28
           EA FLA E D      I V
Sbjct: 146 EALFLAREVDPNGKRTIGV 164


>gnl|CDD|111813 pfam02965, Met_synt_B12, Vitamin B12 dependent methionine
          synthase, activation domain. 
          Length = 126

 Score = 24.6 bits (54), Expect = 5.9
 Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 2/33 (6%)

Query: 39 IQKYFFMDALENQLKEARFLAEEADKKYDETAG 71
            K   +DAL + L EA  LAE   K+  +  G
Sbjct: 28 DYKAIIVDALGSALAEA--LAEYLHKRLRKEWG 58


>gnl|CDD|239019 cd02068, radical_SAM_B12_BD, B12 binding domain_like associated
          with radical SAM domain. This domain shows similarity
          with B12 (adenosylcobamide) binding domains found in
          several enzymes, such as glutamate mutase, methionine
          synthase and methylmalonyl-CoA mutase, but it lacks the
          signature motif Asp-X-His-X-X-Gly, which contains the
          histidine that acts as a cobalt ligand. The function of
          this domain remains unclear.
          Length = 127

 Score = 24.6 bits (54), Expect = 6.0
 Identities = 12/34 (35%), Positives = 16/34 (47%)

Query: 7  QLKEARFLAEEADKKYDEVIFVCGNRERRFFPIQ 40
           + EA  LA+ A +    VI V G     FFP +
Sbjct: 51 AIYEALELAKIAKEVLPNVIVVVGGPHATFFPEE 84


>gnl|CDD|235099 PRK03011, PRK03011, butyrate kinase; Provisional.
          Length = 358

 Score = 25.1 bits (56), Expect = 6.2
 Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)

Query: 3   ALENQLKEARFLAEEADKKYDEVIFV 28
           AL NQ   AR +A+E  KKY+E+  +
Sbjct: 155 AL-NQKAVARRVAKELGKKYEELNLI 179


>gnl|CDD|147776 pfam05804, KAP, Kinesin-associated protein (KAP).  This family
           consists of several eukaryotic kinesin-associated (KAP)
           proteins. Kinesins are intracellular multimeric
           transport motor proteins that move cellular cargo on
           microtubule tracks. It has been shown that the sea
           urchin KRP85/95 holoenzyme associates with a KAP115
           non-motor protein, forming a heterotrimeric complex in
           vitro, called the Kinesin-II.
          Length = 708

 Score = 24.8 bits (54), Expect = 8.1
 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 10/65 (15%)

Query: 11  ARFLAEEADKKYDEV-----IFVCGNRERRFFPIQKYFF-----MDALENQLKEARFLAE 60
           AR L E+  K  +       IF C +   +F P+  ++      M+ +E++LK   F  E
Sbjct: 166 ARVLREDWKKSVELATNIIYIFFCFSSFSQFHPLIVHYKIGALCMNVIEHELKRYEFWIE 225

Query: 61  EADKK 65
           E DKK
Sbjct: 226 ELDKK 230


  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
   0.323    0.139    0.399 

Gapped
Lambda     K      H
   0.267   0.0716    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,828,683
Number of extensions: 419064
Number of successful extensions: 590
Number of sequences better than 10.0: 1
Number of HSP's gapped: 584
Number of HSP's successfully gapped: 35
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)