RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1002
         (136 letters)



>gnl|CDD|203677 pfam07542, ATP12, ATP12 chaperone protein.  Mitochondrial F1-ATPase
           is an oligomeric enzyme composed of five distinct
           subunit polypeptides. The alpha and beta subunits make
           up the bulk of protein mass of F1. In Saccharomyces
           cerevisiae both subunits are synthesised as precursors
           with amino-terminal targeting signals that are removed
           upon translocation of the proteins to the matrix
           compartment. These proteins include examples from
           eukaryotes and bacteria and may have chaperone activity,
           being involved in F1 ATPase complex assembly.
          Length = 122

 Score =  131 bits (331), Expect = 2e-40
 Identities = 44/98 (44%), Positives = 60/98 (61%), Gaps = 1/98 (1%)

Query: 30  KRFYKKVGILESNGDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQHETIQRSTM 89
           KRFYK+V + E  G + + LD R +KTP      V SE LA AIAAEWDAQ E I  +TM
Sbjct: 1   KRFYKEVSVEEEEGGFAVLLDGRPVKTPAKNPLAVPSEALAEAIAAEWDAQGEVIDPATM 60

Query: 90  HLTAICNTVIDNPNRLTKFDLVQNIINFLDTDTILYHA 127
            LT + NT ID      +  ++++++ +LDTD + Y A
Sbjct: 61  PLTRLANTAIDLVA-EDRDAVIEDLLRYLDTDLLCYRA 97


>gnl|CDD|227677 COG5387, COG5387, Chaperone required for the assembly of the
           mitochondrial F1-ATPase [Posttranslational modification,
           protein turnover, chaperones].
          Length = 264

 Score = 80.6 bits (199), Expect = 2e-19
 Identities = 44/100 (44%), Positives = 55/100 (55%), Gaps = 2/100 (2%)

Query: 29  PKRFYKKVGILES-NGDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQHETIQRS 87
           PKRFYKK    +   G + I LD R LKTP G    V +E LA  +A EWDAQ E+I   
Sbjct: 32  PKRFYKKATAADVEKGGFAIQLDGRTLKTPAGKPLVVPTEALAYLLALEWDAQSESIDPH 91

Query: 88  TMHLTAICNTVIDNPNRLTKFDLVQNIINFLDTDTILYHA 127
           +M LT + NT ID         + + I+ FLDTD + Y A
Sbjct: 92  SMPLTRLVNTAIDGI-AEDSQAVFEQILRFLDTDLLCYRA 130


>gnl|CDD|139876 PRK13814, pyrB, aspartate carbamoyltransferase catalytic subunit;
           Provisional.
          Length = 310

 Score = 27.8 bits (61), Expect = 2.1
 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 10/86 (11%)

Query: 22  KYSALEKPKRFYKKVGILESNGDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQH 81
           K SA+ K +  +  +  LE+ G Y   + H + +TP  +  ++SS    +  A + + QH
Sbjct: 80  KISAISKGETLFDTIKTLEAMGVYFFIVRHSENETPEQIAKQLSSG--VVINAGDGNHQH 137

Query: 82  E--------TIQRSTMHLTAICNTVI 99
                    TI++   H   +C T+I
Sbjct: 138 PSQALIDLMTIKQHKPHWNKLCVTII 163


>gnl|CDD|143171 cd04970, Ig6_Contactin_like, Sixth Ig domain of contactin.
          Ig6_Contactin_like: Sixth Ig domain of contactins.
          Contactins are neural cell adhesion molecules and are
          comprised of six Ig domains followed by four
          fibronectin type III(FnIII) domains anchored to the
          membrane by glycosylphosphatidylinositol. The first
          four Ig domains form the intermolecular binding
          fragment, which arranges as a compact U-shaped module
          via contacts between Ig domains 1 and 4, and between Ig
          domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play
          a part in the neuronal processes of neurite outgrowth,
          axon guidance and fasciculation, and neuronal
          migration. This group also includes contactin-1 and
          contactin-5. The different contactins show different
          expression patterns in the central nervous system.
          During development and in adulthood, contactin-2 is
          transiently expressed in subsets of central and
          peripheral neurons. Contactin-5 is expressed
          specifically in the rat postnatal nervous system,
          peaking at about 3 weeks postnatal, and a lack of
          contactin-5 (NB-2) results in an impairment of neur
          onal act ivity in the rat auditory system. Contactin-5
          is highly expressed in the adult human brain in the
          occipital lobe and in the amygdala. Contactin-1 is
          differentially expressed in tumor tissues and may,
          through a RhoA mechanism, facilitate invasion and
          metastasis of human lung adenocarcinoma.
          Length = 85

 Score = 25.9 bits (57), Expect = 3.0
 Identities = 9/22 (40%), Positives = 13/22 (59%)

Query: 26 LEKPKRFYKKVGILESNGDYEI 47
           +K    Y++VG  +SNGD  I
Sbjct: 30 FDKDGGHYRRVGGKDSNGDLMI 51


>gnl|CDD|222555 pfam14119, DUF4288, Domain of unknown function (DUF4288).  This
          family of proteins is functionally uncharacterized.
          This family of proteins is found in bacteria. Proteins
          in this family are approximately 120 amino acids in
          length.
          Length = 87

 Score = 26.1 bits (58), Expect = 3.4
 Identities = 14/52 (26%), Positives = 19/52 (36%)

Query: 32 FYKKVGILESNGDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQHET 83
          +Y    I E   + +   D R L     VL K  SE  A   A +   + E 
Sbjct: 1  WYVVKLIYEIIDENKGVEDDRPLFEERIVLVKADSEEEAYEKAEKIAKEEEE 52


>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
          Length = 763

 Score = 26.8 bits (59), Expect = 5.2
 Identities = 8/12 (66%), Positives = 10/12 (83%)

Query: 43  GDYEISLDHRKL 54
           G YE+ L+HRKL
Sbjct: 474 GTYEVKLNHRKL 485


>gnl|CDD|225789 COG3250, LacZ, Beta-galactosidase/beta-glucuronidase
          [Carbohydrate transport and metabolism].
          Length = 808

 Score = 26.2 bits (58), Expect = 6.9
 Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 5/60 (8%)

Query: 23 YSALEKPKRFYKKVGILESNGDYEISLDHRKLKTPNGVLFKVSSEPLALAIAAEWDAQHE 82
             +E P R  K +     NG +  SLD      P      + SE  A+A+   W  Q E
Sbjct: 2  LRPVETPSREIKSL-----NGLWAFSLDDEPCAVPQRWPESLLSESRAIAVPGNWQDQGE 56


>gnl|CDD|116027 pfam07405, DUF1506, Protein of unknown function (DUF1506).  This
          family consists of several bacterial proteins of around
          130 residues in length. Members of this family seem to
          be specific to Borrelia burgdorferi (Lyme disease
          spirochete). The function of this family is unknown.
          Length = 133

 Score = 25.4 bits (55), Expect = 8.9
 Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 28 KPKRFYKKVGI-LESNGDYEISLDHRKLKTPNGVLFKVSSEPLAL 71
          KP +FYK   + LE++  Y+   D  K     GV+  +  + LA+
Sbjct: 29 KPLKFYKGTVVKLENDSSYQRVFDKNKYTEFAGVIIDIKPQELAI 73


>gnl|CDD|234769 PRK00451, PRK00451, glycine dehydrogenase subunit 1; Validated.
          Length = 447

 Score = 25.5 bits (57), Expect = 9.9
 Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 3/25 (12%)

Query: 58  NGVLFKVSSEPLALAI---AAEWDA 79
            G LF V  +P++L +     E+ A
Sbjct: 232 GGALFIVGVDPVSLGLLKPPGEYGA 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
   0.322    0.136    0.401 

Gapped
Lambda     K      H
   0.267   0.0729    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,727,074
Number of extensions: 577937
Number of successful extensions: 473
Number of sequences better than 10.0: 1
Number of HSP's gapped: 470
Number of HSP's successfully gapped: 20
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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: 54 (24.6 bits)