RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13558
         (73 letters)



>gnl|CDD|215754 pfam00153, Mito_carr, Mitochondrial carrier protein. 
          Length = 96

 Score = 54.6 bits (132), Expect = 1e-11
 Identities = 19/62 (30%), Positives = 29/62 (46%)

Query: 1  MKTIDGKPEFKGAFDVLGKVIKQEGVLALWKGFMPYFLRIGPHTVLTFIFLEQMCIFYNK 60
               G  ++KG  D   K+ K+EG+  L+KG +P  LR+ P   + F   E +     K
Sbjct: 35 SSAAGGSRKYKGILDCFKKIYKEEGIRGLYKGLLPNLLRVAPAAAIYFGTYETLKKLLLK 94

Query: 61 KF 62
          K 
Sbjct: 95 KL 96


>gnl|CDD|240302 PTZ00169, PTZ00169, ADP/ATP transporter on adenylate translocase;
           Provisional.
          Length = 300

 Score = 37.8 bits (88), Expect = 1e-04
 Identities = 15/29 (51%), Positives = 19/29 (65%)

Query: 6   GKPEFKGAFDVLGKVIKQEGVLALWKGFM 34
           G  EF G FD L K+ KQ G L+L++GF 
Sbjct: 149 GDREFTGLFDCLMKISKQTGFLSLYQGFG 177



 Score = 35.5 bits (82), Expect = 6e-04
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 3/57 (5%)

Query: 8   PEFKGAFDVLGKVIKQEGVLALWKGFMPYFLRIGPHTVLTFIF---LEQMCIFYNKK 61
           P + G  +   +V K++GVL+LW+G     +R  P     F F    + M   YN+K
Sbjct: 50  PRYSGIVNCFRRVSKEQGVLSLWRGNTANVIRYFPTQAFNFAFKDYFKNMFPKYNQK 106



 Score = 27.8 bits (62), Expect = 0.44
 Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 1/40 (2%)

Query: 10  FKGAFDVLGKVIKQEGVLALWKGFMPYFLR-IGPHTVLTF 48
           + G  D   K++K EG+   +KG     LR  G   VL F
Sbjct: 252 YTGTLDCWKKILKNEGLGGFFKGAWANVLRGAGGALVLVF 291


>gnl|CDD|132396 TIGR03353, VI_chp_4, type VI secretion protein, VC_A0114 family.
           Work by Mougous, et al. (2006), describes IAHP-related
           loci as a type VI secretion system (PMID:16763151). This
           protein family is associated with type VI secretion
           loci, although not treated explicitly by Mougous, et al
           [Protein fate, Protein and peptide secretion and
           trafficking, Cellular processes, Pathogenesis].
          Length = 439

 Score = 28.0 bits (63), Expect = 0.34
 Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 5/51 (9%)

Query: 9   EFKGAFDVLG----KVIKQEGVLALWKGFMPYFLRIGPHTVLTFIFLEQMC 55
           E    +  L     K ++ +G + L   F+P  L IG    L    L ++ 
Sbjct: 153 EDLSGYVSLPIARIKEVRADGGIILDPSFIPPCLSIGASPPLG-QRLRELL 202


>gnl|CDD|201133 pfam00289, CPSase_L_chain, Carbamoyl-phosphate synthase L chain,
           N-terminal domain.  Carbamoyl-phosphate synthase
           catalyzes the ATP-dependent synthesis of
           carbamyl-phosphate from glutamine or ammonia and
           bicarbonate. This important enzyme initiates both the
           urea cycle and the biosynthesis of arginine and/or
           pyrimidines. The carbamoyl-phosphate synthase (CPS)
           enzyme in prokaryotes is a heterodimer of a small and
           large chain. The small chain promotes the hydrolysis of
           glutamine to ammonia, which is used by the large chain
           to synthesise carbamoyl phosphate. See pfam00988. The
           small chain has a GATase domain in the carboxyl
           terminus. See pfam00117.
          Length = 108

 Score = 26.3 bits (59), Expect = 0.80
 Identities = 9/46 (19%), Positives = 16/46 (34%), Gaps = 9/46 (19%)

Query: 19  KVIKQEGVLALWKGFMPYFLRIGPHTVLTFIFLEQMCIFYNKKFMG 64
            + ++EG  A+  G+   FL              + C      F+G
Sbjct: 67  DIAEKEGADAIHPGYG--FLSENAE-------FAEACEEAGITFIG 103


>gnl|CDD|212087 cd11518, SLC6sbd_SIT1, Na(+)- and Cl(-)-dependent imino acid
           transporter SIT1; solute-binding domain.  SIT1 (also
           called XTRP3, XT3, IMINO) transports imino acids, such
           as proline, pipecolate, MeAIB, and sarcosine. It has
           weak affinity for neutral amino acids such as
           phenylalanine. Human SIT1 is encoded by the SLC6A20
           gene. SIT1 is expressed in brain, kidney, small
           intestine, thymus, spleen, ovary, and lung. SLC6A20 is a
           candidate gene for the rare disorder iminoglycinuria.
           This subgroup belongs to the solute carrier 6 (SLC6)
           transporter family.
          Length = 576

 Score = 26.3 bits (58), Expect = 1.3
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 5/59 (8%)

Query: 1   MKTIDGKPEFKGAFDVLGKVIKQEGVLALWKGFMPYFLRIGPHTVLTFIFLEQMCIFYN 59
           M  ++G P       V G+ ++Q G +  WK   PY   +G  +V+   FL    ++YN
Sbjct: 49  MLILEGMPLLYLELAV-GQRMRQ-GSIGAWKSISPYLGGVGVASVVVSFFL---SMYYN 102


>gnl|CDD|177990 PLN02361, PLN02361, alpha-amylase.
          Length = 401

 Score = 24.8 bits (54), Expect = 4.2
 Identities = 18/52 (34%), Positives = 21/52 (40%), Gaps = 6/52 (11%)

Query: 4   IDGKPEFKGAFDVLGKVIKQEGVLALW------KGFMPYFLRIGPHTVLTFI 49
           IDG      AFD   K I QE V   W      +G  P  +   P   +TFI
Sbjct: 233 IDGTGGLSAAFDFTTKGILQEAVKGQWWRLRDAQGKPPGVMGWWPSRAVTFI 284


>gnl|CDD|99822 cd05779, DNA_polB_epsilon_exo, DEDDy 3'-5' exonuclease domain of
          eukaryotic DNA polymerase epsilon, a family-B DNA
          polymerase.  The 3'-5' exonuclease domain of eukaryotic
          DNA polymerase epsilon. DNA polymerase epsilon is a
          family-B DNA polymerase with a catalytic subunit that
          contains a DEDDy-type DnaQ-like 3'-5' exonuclease
          domain. It is one of the three DNA-dependent type B DNA
          polymerases (alpha and delta are the other two) that
          have been identified as essential for nuclear DNA
          replication in eukaryotes. DNA polymerase epsilon plays
          a role in elongating the leading strand during DNA
          replication. It is also involved in DNA repair. The
          catalytic subunit contains both polymerase and 3'-5'
          exonuclease activities. The N-terminal exonuclease
          domain contains three sequence motifs termed ExoI,
          ExoII and ExoIII, with a specific YX(3)D pattern at
          ExoIII. These motifs are clustered around the active
          site and are involved in metal binding and catalysis.
          DNA polymerase epsilon also carries a unique large
          C-terminal domain with an unknown function.
          Phylogenetic analyses indicate that it is orthologous
          to the archaeal DNA polymerase B3 rather than to the
          eukaryotic alpha, delta, or zeta polymerases. The
          exonuclease domain of family-B polymerases contains a
          beta hairpin structure that plays an important role in
          active site switching in the event of nucleotide
          misincorporation.
          Length = 204

 Score = 23.8 bits (52), Expect = 9.5
 Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 4/42 (9%)

Query: 7  KPEFKGAFDVLGKVIKQEGVLALWKGFMPYFLRIGPHTVLTF 48
          KPE++G F    KV  +    AL + F  +   + PH ++T+
Sbjct: 58 KPEYEGPF----KVFNEPDEKALLQRFFEHIREVKPHIIVTY 95


  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
   0.327    0.146    0.459 

Gapped
Lambda     K      H
   0.267   0.0810    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,812,982
Number of extensions: 298296
Number of successful extensions: 284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 13
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
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 (24.0 bits)