RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11215
         (100 letters)



>gnl|CDD|217512 pfam03359, GKAP, Guanylate-kinase-associated protein (GKAP)
           protein. 
          Length = 342

 Score = 68.7 bits (168), Expect = 3e-15
 Identities = 27/65 (41%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 31  KDTNIPEDIRDEIDCVVGQTKLLTSDKFQQMSNLIDQYENQSEQAQPRILENDLDSFWDM 90
           ++  +PE++   I   VGQ +LL S KFQQ   L DQ  N    A+PR    DL  FWDM
Sbjct: 188 EENELPEEVLGLIRTAVGQARLLMSQKFQQFEGLCDQNLNPR--AEPRTTSQDLAGFWDM 245

Query: 91  IYIQL 95
           + +Q+
Sbjct: 246 LQLQI 250


>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
          Length = 812

 Score = 32.2 bits (74), Expect = 0.024
 Identities = 8/22 (36%), Positives = 12/22 (54%)

Query: 67  QYENQSEQAQPRILENDLDSFW 88
           Q E  + Q++P IL +DL    
Sbjct: 340 QAERAAAQSEPEILHSDLSGLL 361


>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
           This family consists of the archaeal A' subunit of the
           DNA-directed RNA polymerase. The example from
           Methanocaldococcus jannaschii contains an intein.
          Length = 867

 Score = 29.7 bits (67), Expect = 0.20
 Identities = 16/61 (26%), Positives = 34/61 (55%), Gaps = 8/61 (13%)

Query: 26  FITPPKDTNIPEDIRDEIDCVVGQTKLLTSDKFQQMSNLIDQYENQSEQAQP-RILENDL 84
           F T   D +IP++ ++EI+ ++ + +       +++ NLI++Y N   +  P R +E  L
Sbjct: 639 FTTGIDDIDIPKEAKEEIEELIEKAE-------KRVDNLIERYRNGELEPLPGRTVEETL 691

Query: 85  D 85
           +
Sbjct: 692 E 692


>gnl|CDD|131830 TIGR02783, TrbL_P, P-type conjugative transfer protein TrbL.  The
          TrbL protein is found in the trb locus of Agrobacterium
          Ti plasmids where it is involved in the type IV
          secretion system for plasmid conjugative transfer. TrbL
          is a homolog of the F-type TraG protein (which is
          believed to be a mating pair stabilization pore-forming
          protein, pfam07916) as well as the vir system VirB6
          protein [Cellular processes, Conjugation].
          Length = 298

 Score = 29.3 bits (66), Expect = 0.25
 Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 4/40 (10%)

Query: 60 QMSNLIDQYENQ----SEQAQPRILENDLDSFWDMIYIQL 95
          Q   ++DQ  +     ++  + RIL   LD FW +  I++
Sbjct: 2  QNVGVLDQLLSLFHTAADIWEGRILIAALDLFWLLAVIEI 41


>gnl|CDD|236815 PRK10997, yieM, hypothetical protein; Provisional.
          Length = 487

 Score = 27.6 bits (62), Expect = 1.00
 Identities = 16/71 (22%), Positives = 39/71 (54%), Gaps = 12/71 (16%)

Query: 17  WKASLRKNSFITPPKDTNIPEDIRDEIDCVVGQTKLLTSDKF-QQMSNLIDQYENQ---- 71
           W+ +LR+       KD  +P ++ +E      Q++LL++ +F  Q+ +++D+        
Sbjct: 53  WREALRQRL-----KDACVPPELAEEFAL-YQQSQLLSTPQFIVQLPDILDKLHRLHSPF 106

Query: 72  SEQAQPRILEN 82
           +EQA+ ++++ 
Sbjct: 107 AEQAR-QLVDA 116


>gnl|CDD|148033 pfam06188, HrpE, HrpE/YscL/FliH and V-type ATPase subunit E.
          This is a prokaryotic family that contains proteins of
          the FliH and HrpE/YscL family. These proteins are
          involved in type III secretion, which is the process
          that drives flagellar biosynthesis and mediates
          bacterial-eukaryotic interactions. This family also
          V-type ATPase subunit E. This subunit appears to form a
          tight interaction with subunit G in the F0 complex.
          Subunits E and G may act together as stators to prevent
          certain subunits from rotating with the central rotary
          element. pfam01991 also contains V-type ATPase subunit
          E proteins.
          Length = 191

 Score = 27.4 bits (61), Expect = 1.1
 Identities = 18/69 (26%), Positives = 26/69 (37%), Gaps = 1/69 (1%)

Query: 21 LRKNSFITPPKDTNIPED-IRDEIDCVVGQTKLLTSDKFQQMSNLIDQYENQSEQAQPRI 79
          L K S         + E  +R E        + L  D  QQ   ++D  E ++E  Q R 
Sbjct: 2  LTKRSITLTNGAAVLEEPVLRREQLAQSLLARTLLEDARQQAEQILDLAEEKAEALQQRA 61

Query: 80 LENDLDSFW 88
           E    +FW
Sbjct: 62 EEQAEAAFW 70


>gnl|CDD|100009 cd06152, YjgF_YER057c_UK114_like_4, YjgF, YER057c, and UK114
          belong to a large family of proteins present in
          bacteria, archaea, and eukaryotes with no definitive
          function.  The conserved domain is similar in structure
          to chorismate mutase but there is no sequence
          similarity and no functional connection. Members of
          this family have been implicated in isoleucine (Yeo7,
          Ibm1, aldR) and purine (YjgF) biosynthesis, as well as
          threonine anaerobic degradation (tdcF) and
          mitochondrial DNA maintenance (Ibm1). This domain
          homotrimerizes forming a distinct intersubunit cavity
          that may serve as a small molecule binding site.
          Length = 114

 Score = 25.3 bits (56), Expect = 3.9
 Identities = 8/15 (53%), Positives = 10/15 (66%)

Query: 30 PKDTNIPEDIRDEID 44
          P    IPED+ +EID
Sbjct: 23 PDTGKIPEDLEEEID 37


>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
           Validated.
          Length = 882

 Score = 26.0 bits (58), Expect = 4.5
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 8/56 (14%)

Query: 32  DTNIPEDIRDEIDCVVGQTKLLTSDKFQQMSNLIDQYENQSEQAQP-RILENDLDS 86
           D +IPE+ ++EID ++ + +       +++  LI+ YEN   +  P R LE  L+ 
Sbjct: 651 DEDIPEEAKEEIDEIIEEAE-------KRVEELIEAYENGELEPLPGRTLEETLEM 699


>gnl|CDD|148650 pfam07163, Pex26, Pex26 protein.  This family consists of Pex26 and
           related mammalian proteins. Pex26 is a type II
           peroxisomal membrane protein which recruits Pex6-Pex1
           complexes to peroxisomes. Mutations in Pex26 can lead to
           human disorders.
          Length = 309

 Score = 25.7 bits (56), Expect = 5.0
 Identities = 12/37 (32%), Positives = 22/37 (59%)

Query: 45  CVVGQTKLLTSDKFQQMSNLIDQYENQSEQAQPRILE 81
           CVVG   L   D+++++ + + QY    E+  P++LE
Sbjct: 86  CVVGIQALAEMDRWREVLSWVLQYYQVPEKLPPKVLE 122


>gnl|CDD|232846 TIGR00153, TIGR00153, TIGR00153 family protein.  An apparent
           homolog with a suggested function is Pit accessory
           protein from Sinorhizobium meliloti, which may be
           involved in phosphate (Pi) transport [Hypothetical
           proteins, Conserved].
          Length = 216

 Score = 25.5 bits (56), Expect = 5.6
 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 7/66 (10%)

Query: 35  IPEDIRDEIDCVVGQTKLLTSDKFQQMSNLIDQYENQS--EQAQPRILE-NDLDSFWDMI 91
            PE++RDE   V+     +T D  Q +  +++  E ++    A   I E  DL+   D++
Sbjct: 111 FPEELRDEFLLVL----KITVDMIQHLHRVVEVIELETDLSLANDIIKEIKDLEDEIDVM 166

Query: 92  YIQLYT 97
            I++Y 
Sbjct: 167 QIRIYK 172


>gnl|CDD|225599 COG3057, SeqA, Negative regulator of replication initiationR [DNA
          replication, recombination, and repair].
          Length = 181

 Score = 24.8 bits (54), Expect = 7.4
 Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 2/40 (5%)

Query: 29 PPKDTNIPEDIRDEIDCVVGQTKLLTSDKFQQMSNLIDQY 68
          P K    P   +   D V    +LL SD++ +    ++++
Sbjct: 54 PAKVEAKPT--KTIKDKVRAMRELLLSDEYAEQKRAVNRF 91


>gnl|CDD|220230 pfam09419, PGP_phosphatase, Mitochondrial PGP phosphatase.  This
          is a family of proteins that acts as a mitochondrial
          phosphatase in cardiolipin biosynthesis. Cardiolipin is
          a unique dimeric phosphoglycerolipid predominantly
          present in mitochondrial membranes. The inverted
          phosphatase motif includes the highly conserved DKD
          triad.
          Length = 166

 Score = 25.0 bits (55), Expect = 7.9
 Identities = 10/40 (25%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 6  EIPEVFVKRKSWKA-SLRKNSFITPPKDTNIPEDIRDEID 44
          ++P   +K+   KA  L K++ +T P D  I    +++ +
Sbjct: 28 QLPIPILKKVGIKAVVLDKDNCLTLPHDDKIWPPYQEKWE 67


>gnl|CDD|240353 PTZ00309, PTZ00309, glucose-6-phosphate 1-dehydrogenase;
           Provisional.
          Length = 542

 Score = 25.1 bits (55), Expect = 8.9
 Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 14/34 (41%)

Query: 29  PPKDTNIPEDIRDE-------------IDCVVGQ 49
            P   +  EDIRDE              +CV+GQ
Sbjct: 305 KPVSLS-AEDIRDEKVKVLKCIEPIKMEECVLGQ 337


>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
           subunit; Provisional.
          Length = 1321

 Score = 25.0 bits (54), Expect = 9.7
 Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 24/81 (29%)

Query: 26  FITPPKDTNIPEDIRDEIDCVVGQTKLLTSDKFQQMSNLIDQYEN--------------- 70
           F   P D  IP++ + EI+  +   K        ++S+LIDQ +                
Sbjct: 665 FSNGPGDLIIPDEAKQEIEDDIQGMK-------DEVSDLIDQRKITRKITIYKGKEELLR 717

Query: 71  --QSEQAQPRILENDLDSFWD 89
             + E+A    + N+LD   D
Sbjct: 718 GMKEEEALEADIVNELDKARD 738


  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
   0.315    0.132    0.380 

Gapped
Lambda     K      H
   0.267   0.0703    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,995,145
Number of extensions: 398706
Number of successful extensions: 462
Number of sequences better than 10.0: 1
Number of HSP's gapped: 461
Number of HSP's successfully gapped: 34
Length of query: 100
Length of database: 10,937,602
Length adjustment: 66
Effective length of query: 34
Effective length of database: 8,010,238
Effective search space: 272348092
Effective search space used: 272348092
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.2 bits)