RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13866
         (201 letters)



>gnl|CDD|221056 pfam11277, Med24_N, Mediator complex subunit 24 N-terminal.  This
           subunit of the Mediator complex appears to be conserved
           only from insects to humans. It is essential for correct
           retinal development in fish. Subunit composition of the
           mediator contributes to the control of differentiation
           in the vertebrate CNS as there are divergent functions
           of the mediator subunits Crsp34/Med27, Trap100/Med24,
           and Crsp150/Med14.
          Length = 991

 Score =  232 bits (593), Expect = 3e-71
 Identities = 107/198 (54%), Positives = 139/198 (70%), Gaps = 4/198 (2%)

Query: 2   IICAEPTLARVLRTLDTEFSKIQDALLNVLSQVLNGKSFDLILAVAAVEGKLCTFVTKLI 61
           I+ AEP L  +L+TLD + SK+Q+ LL VL QVL+G S DL+L+VAAVEGKL +F  KLI
Sbjct: 414 ILRAEPPLTGILKTLDADHSKVQEGLLGVLCQVLSGNSLDLLLSVAAVEGKLKSFARKLI 473

Query: 62  KFNECSKQSNPSDTSKTAQTKVMLFDITFLMLCSIVQRYGSKVVFSENGGDSFFEKWVRD 121
           K NE SK   P ++ K A  + +LFD++FLMLC IVQ YGS+V+ SE GGDSFFEKWVR 
Sbjct: 474 KCNEFSKHV-PGESGKAASVRALLFDVSFLMLCHIVQTYGSEVILSE-GGDSFFEKWVRT 531

Query: 122 CMVEGGRPKPYKKMLDEKDQAGVDDLLRQFNSSDAEFKNCPKLNCYEICLNIPAVIYDVL 181
           CMVE G+ K         D + V++L+   N+S+ E K   +L  +EICL+IPA I +VL
Sbjct: 532 CMVEEGKTKNPDHPCFRPDSSKVEELVALLNNSE-ELK-LVQLKWHEICLSIPAAILEVL 589

Query: 182 GAWETSVLSSTDVKRILD 199
            AWE  VLSS ++K+ILD
Sbjct: 590 NAWENEVLSSEEIKKILD 607


>gnl|CDD|235564 PRK05691, PRK05691, peptide synthase; Validated.
          Length = 4334

 Score = 29.8 bits (67), Expect = 1.3
 Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 3/38 (7%)

Query: 17   DTEFSKIQDALLNVLSQVLNGKSFDLILAVAAVEGKLC 54
            D E S I   L NVL +VL+    +L L    V G+LC
Sbjct: 1439 DGERSPIGRPLGNVLCRVLDA---ELNLLPPGVAGELC 1473


>gnl|CDD|213314 cd05967, PrpE, Propionyl-CoA synthetase (PrpE).  PrpE catalyzes the
           first step of the 2-methylcitric acid cycle for
           propionate catabolism. It activates propionate to
           propionyl-CoA in a two-step reaction, which proceeds
           through a propionyl-AMP intermediate and requires ATP
           and Mg2+. In Salmonella enterica, the PrpE protein is
           required for growth of S. enterica on propionate and can
           substitute for the acetyl-CoA synthetase (Acs) enzyme
           during growth on acetate. PrpE can also activate
           acetate, 3HP, and butyrate to their corresponding
           CoA-thioesters, although with less efficiency.
          Length = 607

 Score = 28.8 bits (65), Expect = 2.2
 Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 12/46 (26%)

Query: 93  LCSIVQRYGSKVVFSENGGDSFFEKWVRDCMVEGGRPKPYKKMLDE 138
           L S +     K++ + + G            +E GR  PYK +LD+
Sbjct: 137 LASRIDDAKPKLIVTASFG------------IEPGRVVPYKPLLDK 170


>gnl|CDD|151967 pfam11530, Pilin_PilX, Minor type IV pilin, PilX.  PilX is a
           protein from Neissaria meningitidis which is crucial for
           the formation of bacterial aggregates and adhesion to
           human cells. The structure of PilX is similar to all
           pilins as it has the common alpha/beta roll fold. PilX
           subunits have surface-exposed motifs which are thought
           to stabilise bacterial aggregates against pilus
           retraction. It also illustrates how a minor pilus
           component can modulate the virulence properties of pili
           which have a simple composition and structure.
          Length = 127

 Score = 27.7 bits (61), Expect = 2.7
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 58  TKLIKFNECSKQ---SNPSDTSKTAQTKVMLFDITFLMLCSIVQRYGSKVVF 106
           T+++  N   KQ    NP D + T ++K+ +F   + M   I ++Y   V F
Sbjct: 13  TEMVGINNILKQFILKNPLDDNDTIKSKLEIFVSGYKMNPKIAEKYNVSVHF 64


>gnl|CDD|240427 PTZ00470, PTZ00470, glycoside hydrolase family 47 protein;
           Provisional.
          Length = 522

 Score = 28.5 bits (64), Expect = 2.8
 Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 14/97 (14%)

Query: 53  LCTFVTKLIKFNECSKQSNPSDTSKTAQTKVMLFDITFLMLCSIVQRYGSKVVFSENG-- 110
           L    T  ++FN  S+ +           KVM  D  F M  +I   Y   +        
Sbjct: 221 LSEVGTLQLEFNYLSEITG-DPKYAEYVDKVM--DALFSMKPAINGLYPIFLNPDAGRFC 277

Query: 111 ---------GDSFFEKWVRDCMVEGGRPKPYKKMLDE 138
                    GDS++E  ++  +   GR + Y+++  E
Sbjct: 278 GNHISLGALGDSYYEYLLKQWLYTNGREERYRRLFVE 314


>gnl|CDD|240614 cd12794, Hsm3_like, Hsm3 is a  yeast Proteasome chaperone of the
          19S regulatory particle and related proteins.  This
          group contains proteins related to the Hsm3 protein
          (Yeast Proteasome Interacting Protein) of Saccharomyces
          cerevisiae. S. cerevisiae Hsm3 is a chaperone of
          regulatory particles involved in proteasome assembly.
          The 26S Proteasome is a large, 2.5 MDa complex
          comprised of at least 33 subunits, and relies on
          chaperones to facilitate correct assembly. The
          proteasome contains a cylindrical 20S core particle and
          1-2 19S regulatory particles, comprised of AAA-ATPase
          and non-ATPase subunits. The proteasome acts in
          ubiquitin-dependent proteolysis. The 19S RP targets and
          opens the the ubiquitin-tagged substrate and releases
          ubiquitin. Hsm3 acts as a 19S chaperone, binding to the
          C-terminal domain of Rpt1 (the 6 ATPase subunits of the
          19 S regulatory particle(s). Hsm3 has a C-shape
          composed of 11 HEAT repeats. Mutations in the Hsm3-Rpt
          interface disrupt formation of the 26 S Proteasome
          complex.
          Length = 455

 Score = 28.0 bits (63), Expect = 4.1
 Identities = 18/46 (39%), Positives = 27/46 (58%), Gaps = 4/46 (8%)

Query: 7  PTLARVLRTLDTEFSKIQD--ALLNVLSQVLNGKSFDLILAVAAVE 50
          P +  +L  LD E  +I D   LL +L ++L+  SFD IL V ++E
Sbjct: 47 PAIKSIL--LDNESYEILDYDLLLELLDKILSLLSFDDILEVFSLE 90


>gnl|CDD|185056 PRK15101, PRK15101, protease3; Provisional.
          Length = 961

 Score = 27.2 bits (61), Expect = 7.1
 Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 1/28 (3%)

Query: 7   PTLARVLRTL-DTEFSKIQDALLNVLSQ 33
           P     LR +   EF++ Q AL+N L Q
Sbjct: 837 PQAEAKLRAMKPEEFAQYQQALINQLLQ 864


>gnl|CDD|215489 PLN02902, PLN02902, pantothenate kinase.
          Length = 876

 Score = 27.2 bits (60), Expect = 8.5
 Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 3/37 (8%)

Query: 112 DSFFEKWVRDCMVEGGRPKPYKKMLDEKDQAGVDDLL 148
           D+F E+ +      G +PKP+K+ L   D +G D +L
Sbjct: 681 DAFKERMLGS---GGKKPKPHKRALLFVDNSGADVVL 714


  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    0.399 

Gapped
Lambda     K      H
   0.267   0.0725    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,848,627
Number of extensions: 872871
Number of successful extensions: 644
Number of sequences better than 10.0: 1
Number of HSP's gapped: 641
Number of HSP's successfully gapped: 13
Length of query: 201
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 109
Effective length of database: 6,857,034
Effective search space: 747416706
Effective search space used: 747416706
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: 56 (25.4 bits)