RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17946
         (223 letters)



>gnl|CDD|148767 pfam07347, CI-B14_5a, NADH:ubiquinone oxidoreductase subunit B14.5a
           (Complex I-B14.5a).  This family contains the eukaryotic
           NADH:ubiquinone oxidoreductase subunit B14.5a (Complex
           I-B14.5a) (EC:1.6.5.3). This is approximately 100
           residues long, and forms part of a multiprotein complex
           that resides on the inner mitochondrial membrane. The
           main function of the complex is the transport of
           electrons from NADH to ubiquinone, accompanied by
           translocation of protons from the mitochondrial matrix
           to the intermembrane space.
          Length = 97

 Score = 78.7 bits (194), Expect = 3e-19
 Identities = 35/71 (49%), Positives = 41/71 (57%), Gaps = 8/71 (11%)

Query: 87  RLIARL-ARLLGTKRRYKVVVDNPLRFQDYNIVPRTQPLPNLPEGPHHVLSANYYVNRDG 145
            L+ RL   LLG  R++K      LR+ D  I  RTQP P LP+GP H LSANYY  RDG
Sbjct: 2   PLLQRLRNFLLG--RQHK----LALRYAD-GISKRTQPPPKLPDGPSHKLSANYYCTRDG 54

Query: 146 SHEVKPPATLY 156
             EV PP  + 
Sbjct: 55  RREVTPPIDIV 65


>gnl|CDD|197258 cd09161, PLDc_PaCLS_like_2, Putative catalytic domain, repeat 2, of
           Pseudomonas aeruginosa cardiolipin synthase and similar
           proteins.  Putative catalytic domain, repeat 2, of
           Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS)
           and similar proteins. Although PaCLS and similar
           proteins have not been functionally characterized,
           members in this subfamily show high sequence homology to
           bacterial CL synthases, which catalyze the reversible
           phosphatidyl group transfer between two
           phosphatidylglycerol molecules to form CL and glycerol.
           Moreover, PaCLS and other members of this subfamily
           contain two HKD motifs (H-x-K-x(4)-D, where x represents
           any amino acid residue) that characterizes the
           phospholipase D (PLD) superfamily. The two motifs may be
           part of the active site and may be involved in
           phosphatidyl group transfer.
          Length = 176

 Score = 29.9 bits (68), Expect = 0.65
 Identities = 14/28 (50%), Positives = 16/28 (57%)

Query: 69  AGARTVVDNELIGRWYWHRLIARLARLL 96
           A +R V   EL  R  W RL AR+ARL 
Sbjct: 145 AASREVTAAELANRPLWFRLGARVARLF 172


>gnl|CDD|212875 cd11942, SH3_JIP2, Src homology 3 domain of JNK-interacting
          protein 2.  JNK-interacting protein 2 (JIP2) is also
          called Mitogen-activated protein kinase 8-interacting
          protein 2 (MAPK8IP2) or Islet-brain-2 (IB2). It is
          widely expressed in the brain, where it forms complexes
          with fibroblast growth factor homologous factors
          (FHFs), which facilitates activation of the p38delta
          MAPK. JIP2 is enriched in postsynaptic densities and
          may play a role in motor and cognitive function. In
          addition to a JNK binding domain, JIP2 also contains
          SH3 and Phosphotyrosine-binding (PTB) domains. The SH3
          domain of the related protein JIP1 homodimerizes at the
          interface usually involved in proline-rich ligand
          recognition, despite the lack of this motif in the
          domain itself. SH3 domains are protein interaction
          domains that bind to proline-rich ligands with moderate
          affinity and selectivity, preferentially to PxxP
          motifs. They play versatile and diverse roles in the
          cell including the regulation of enzymes, changing the
          subcellular localization of signaling pathway
          components, and mediating the formation of multiprotein
          complex assemblies.
          Length = 55

 Score = 28.0 bits (62), Expect = 0.68
 Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 2/46 (4%)

Query: 12 HFQLFTMVPQHWCSFESSIEYFGLVQCEEKQNWF--FDLLKTKRGI 55
          H  +F  +P+H    E  ++   LV+ EE   W+  +++   +RGI
Sbjct: 2  HRAVFRFIPRHEDELELDVDDPLLVEAEEDDYWYRGYNMRTGERGI 47


>gnl|CDD|236731 PRK10658, PRK10658, putative alpha-glucosidase; Provisional.
          Length = 665

 Score = 27.6 bits (62), Expect = 6.1
 Identities = 10/20 (50%), Positives = 10/20 (50%), Gaps = 2/20 (10%)

Query: 10  LH--HFQLFTMVPQHWCSFE 27
           LH  HF  F M    WC FE
Sbjct: 299 LHVFHFDCFWMKEFQWCDFE 318


>gnl|CDD|143511 cd07376, PLPDE_III_DSD_D-TA_like, Type III Pyridoxal 5-phosphate
           (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase
           and D-Threonine Aldolase.  This family includes
           eukaryotic D-serine dehydratases (DSD), cryptic DSDs
           from bacteria, D-threonine aldolases (D-TA), low
           specificity D-TAs, and similar uncharacterized proteins.
           DSD catalyzes the dehydration of D-serine to
           aminoacrylate, which is rapidly hydrolyzed to pyruvate
           and ammonia. D-TA reversibly catalyzes the aldol
           cleavage of D-threonine into glycine and acetaldehyde,
           and the synthesis of D-threonine from glycine and
           acetaldehyde. Members of this family are fold type III
           PLP-dependent enzymes, similar to bacterial alanine
           racemase (AR), which contains an N-terminal PLP-binding
           TIM barrel domain and a C-terminal beta-sandwich domain.
           AR exists as homodimers with active sites that lie at
           the interface between the TIM barrel domain of one
           subunit and the beta-sandwich domain of the other
           subunit. Based on similarity to AR, it is possible
           members of this family also form dimers in solution.
          Length = 345

 Score = 27.0 bits (60), Expect = 8.3
 Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 5/76 (6%)

Query: 51  TKRGISKTKIERIDTLQNAGARTV-VDNELIGRWYWHRLIARLARLLGTKRRYKVVVDNP 109
             RG++   +   +T   AG + + +   L+G       IARLA LL  +  + V+VD+P
Sbjct: 40  GARGVTVATLAEAETFAEAGVKDILMAYPLVGP---AA-IARLAGLLRQEAEFHVLVDSP 95

Query: 110 LRFQDYNIVPRTQPLP 125
                         + 
Sbjct: 96  EALAALAAFAAAHGVR 111


>gnl|CDD|178283 PLN02679, PLN02679, hydrolase, alpha/beta fold family protein.
          Length = 360

 Score = 27.1 bits (60), Expect = 8.9
 Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 8/45 (17%)

Query: 44  WFFDLLKTKRGISKTKIERI---DTLQNA-----GARTVVDNELI 80
           W  D L  +RGI+     R+   D L+N      G +  VD+EL+
Sbjct: 212 WLIDFLLKQRGIASALFNRVKQRDNLKNILLSVYGNKEAVDDELV 256


  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    0.137    0.420 

Gapped
Lambda     K      H
   0.267   0.0642    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,348,160
Number of extensions: 1059032
Number of successful extensions: 966
Number of sequences better than 10.0: 1
Number of HSP's gapped: 966
Number of HSP's successfully gapped: 16
Length of query: 223
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 130
Effective length of database: 6,812,680
Effective search space: 885648400
Effective search space used: 885648400
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: 57 (25.9 bits)