RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1379
         (446 letters)



>gnl|CDD|221258 pfam11841, DUF3361, Domain of unknown function (DUF3361).  This
           domain is functionally uncharacterized. This domain is
           found in eukaryotes. This presumed domain is typically
           between 154 to 168 amino acids in length.
          Length = 158

 Score =  132 bits (334), Expect = 5e-37
 Identities = 64/147 (43%), Positives = 90/147 (61%), Gaps = 3/147 (2%)

Query: 293 LDCFAVLV-NHSQAGLCVMLAHCLLSFVELMDHGIVSWNILETVFIKTVADHVNNPNPVP 351
           LD    ++   S      +LA  L +FVELM+HGIVSW IL   FIK     VN  +   
Sbjct: 13  LDLLISIIEEGSDPCFGEILAFTLTAFVELMEHGIVSWEILSLSFIKKNISFVNKSSL-- 70

Query: 352 EKEIVQASLSILESIALNSVGKFSQVENHLTLTNLVMHLQNQSPIIQQNAIALINALFIK 411
           +K I+Q +L+ILESI LNS   +  V   +TL +L+ HLQ  +  IQ NAIALINALF+K
Sbjct: 71  DKSILQRALAILESIVLNSPALYQLVAREITLESLLKHLQGSNQEIQTNAIALINALFLK 130

Query: 412 AEPSKRKVISATMCSKQVRNAILTSVL 438
           A+  +R+ ++ T+  KQ+R  IL +++
Sbjct: 131 ADDGERQEMADTLSQKQLRLIILNNII 157



 Score =  127 bits (320), Expect = 5e-35
 Identities = 62/133 (46%), Positives = 85/133 (63%), Gaps = 7/133 (5%)

Query: 1   MLAHCLLSFVELMDHGIVSWNILETVFIKTVADHVNNPNPVPEKEIVQASLSILESIALN 60
           +LA  L +FVELM+HGIVSW IL   FIK     VN  +   +K I+Q +L+ILESI LN
Sbjct: 31  ILAFTLTAFVELMEHGIVSWEILSLSFIKKNISFVNKSSL--DKSILQRALAILESIVLN 88

Query: 61  SVGKFSQFSQ-VENHLTLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATMC 119
           S        Q V   +TL +L+ HLQ  +  IQ NAIALINALF+KA+  +R+ ++ T+ 
Sbjct: 89  S----PALYQLVAREITLESLLKHLQGSNQEIQTNAIALINALFLKADDGERQEMADTLS 144

Query: 120 SKQVRNAILTSVL 132
            KQ+R  IL +++
Sbjct: 145 QKQLRLIILNNII 157


>gnl|CDD|218231 pfam04727, ELMO_CED12, ELMO/CED-12 family.  This family represents
           a conserved domain which is found in a number of
           eukaryotic proteins including CED-12, ELMO I and ELMO
           II. ELMO1 is a component of signalling pathways that
           regulate phagocytosis and cell migration and is the
           mammalian orthologue of the C. elegans gene, ced-12.
           CED-12 is required for the engulfment of dying cells and
           cell migration. In mammalian cells, ELMO1 interacts with
           Dock180 as part of the CrkII/Dock180/Rac pathway
           responsible for phagocytosis and cell migration. ELMO1
           is ubiquitously expressed, although its expression is
           highest in the spleen, an organ rich in immune cells.
           ELMO1 has a PH domain and a polyproline sequence motif
           at its C terminus which are not present in this
           alignment.
          Length = 170

 Score = 86.6 bits (215), Expect = 5e-20
 Identities = 31/97 (31%), Positives = 49/97 (50%), Gaps = 13/97 (13%)

Query: 153 LTLGLLEQRMNTKMDPQDQDAHDKIKELRRVAFEIDVIGGVDASSKRQMGGYAKDYKKLG 212
           LTL LLE+   T  D ++ +    +K L +  F        +  S R     ++ +K LG
Sbjct: 1   LTLNLLEKLRKTPFDLENPEHRRLLKTLWKALF------PDEPLSSR----VSEKWKDLG 50

Query: 213 FKYDINPAQDFTETPPGMLALDCMIYFARNHPEAYTK 249
           F+   +PA DF  T  G+L L  ++YFA N+P+ + K
Sbjct: 51  FQ-GDDPATDFRGT--GLLGLLNLLYFAENYPDEFQK 84


>gnl|CDD|132132 TIGR03088, stp2, sugar transferase, PEP-CTERM/EpsH1 system
           associated.  Members of this family include a match to
           the pfam00534 Glycosyl transferases group 1 domain.
           Nearly all are found in species that encode the
           PEP-CTERM/exosortase system predicted to act in protein
           sorting in a number of Gram-negative bacteria. In
           particular, these transferases are found proximal to a
           particular variant of exosortase, EpsH1, which appears
           to travel with a conserved group of genes summarized by
           Genome Property GenProp0652. The nature of the sugar
           transferase reaction catalyzed by members of this clade
           is unknown and may conceivably be variable with respect
           to substrate by species, but we hypothesize a conserved
           substrate.
          Length = 374

 Score = 31.6 bits (72), Expect = 0.76
 Identities = 14/69 (20%), Positives = 27/69 (39%), Gaps = 4/69 (5%)

Query: 337 IKTVADHVN----NPNPVPEKEIVQASLSILESIALNSVGKFSQVENHLTLTNLVMHLQN 392
           I  + + V+    +P+      I+       ES+ + +VG+   V++  TL      L  
Sbjct: 162 IHQIYNGVDTERFHPSRGDRSPILPPDFFADESVVVGTVGRLQAVKDQPTLVRAFALLVR 221

Query: 393 QSPIIQQNA 401
           Q P   +  
Sbjct: 222 QLPEGAERL 230


>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
           Validated.
          Length = 709

 Score = 28.5 bits (63), Expect = 8.9
 Identities = 30/121 (24%), Positives = 49/121 (40%), Gaps = 10/121 (8%)

Query: 270 PDTDTL---SSDVSG-QVRLYFSIQFLLDCFAVLVNHSQAG----LCVMLAHCLLSFVEL 321
           PD+D L   +  +SG Q++LY+ I         L     AG    L  MLA   L+    
Sbjct: 307 PDSDILHRLAQTISGEQIQLYYQIAVHGKRDLSLAPDEYAGFMMTLLRMLAFAPLAAASC 366

Query: 322 MDHGIVSWNILETVFIKTVADHV--NNPNPVPEKEIVQASLSILESIALNSVGKFSQVEN 379
             + ++    L++   +T         P P PE E  Q  +    + A+ S GK +   +
Sbjct: 367 DANAVIENTELQSPSAQTAEKETAAKKPQPRPEAETAQTPVQTASAAAMPSEGKTAGPVS 426

Query: 380 H 380
           +
Sbjct: 427 N 427


>gnl|CDD|161785 TIGR00239, 2oxo_dh_E1, 2-oxoglutarate dehydrogenase, E1 component. 
           The 2-oxoglutarate dehydrogenase complex consists of
           this thiamine pyrophosphate-binding subunit (E1),
           dihydrolipoamide succinyltransferase (E2), and lipoamide
           dehydrogenase (E3). The E1 ortholog from Corynebacterium
           glutamicum is unusual in having an N-terminal extension
           that resembles the dihydrolipoamide succinyltransferase
           (E2) component of 2-oxoglutarate dehydrogenase [Energy
           metabolism, TCA cycle].
          Length = 929

 Score = 28.3 bits (63), Expect = 9.6
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 5/59 (8%)

Query: 63  GKFSQFSQVEN---HLTLTNLVMHLQNQSPIIQQNAIALINALFIKAEPSKRKVISATM 118
           G+FS     +    HL L     HL+  SP++  +  A ++ L     P   KV++  +
Sbjct: 293 GRFSSDFTTDGKLVHLALAFNPSHLEIVSPVVIGSTRARLDRL--NDSPESTKVLAILI 349


  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
   0.319    0.132    0.372 

Gapped
Lambda     K      H
   0.267   0.0697    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,778,851
Number of extensions: 2087336
Number of successful extensions: 1630
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1626
Number of HSP's successfully gapped: 21
Length of query: 446
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 346
Effective length of database: 6,502,202
Effective search space: 2249761892
Effective search space used: 2249761892
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 (21.8 bits)
S2: 61 (27.3 bits)