RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2304
         (85 letters)



>gnl|CDD|172759 PRK14271, PRK14271, phosphate ABC transporter ATP-binding protein;
           Provisional.
          Length = 276

 Score = 27.4 bits (60), Expect = 0.88
 Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 3/53 (5%)

Query: 36  DRVVVMELIKNVAQTNQLDPNGQRDFKGKFVARGP---LVGNPWHRASSLQIA 85
           DR+ V+ +  N+AQ  ++       F G+ V  GP   L  +P H  ++  +A
Sbjct: 211 DRLTVIIVTHNLAQAARISDRAALFFDGRLVEEGPTEQLFSSPKHAETARYVA 263


>gnl|CDD|185145 PRK15223, PRK15223, pilin outer membrane usher protein SafC;
          Provisional.
          Length = 836

 Score = 26.9 bits (59), Expect = 1.3
 Identities = 11/33 (33%), Positives = 16/33 (48%)

Query: 23 YHIEVNPNDAGIYDRVVVMELIKNVAQTNQLDP 55
          Y ++V  N   +  R VV +L K+   T  L P
Sbjct: 53 YRVDVMVNGKRVDTRDVVFKLEKDGQGTPFLAP 85


>gnl|CDD|226927 COG4555, NatA, ABC-type Na+ transport system, ATPase component
           [Energy production and conversion / Inorganic ion
           transport and metabolism].
          Length = 245

 Score = 26.6 bits (59), Expect = 1.3
 Identities = 10/30 (33%), Positives = 15/30 (50%)

Query: 24  HIEVNPNDAGIYDRVVVMELIKNVAQTNQL 53
            I V   + G+Y R+   E +K  A+ N L
Sbjct: 76  KIGVLFGERGLYARLTARENLKYFARLNGL 105


>gnl|CDD|234936 PRK01293, PRK01293, phosphoribosyl-dephospho-CoA transferase;
           Provisional.
          Length = 207

 Score = 26.0 bits (58), Expect = 2.1
 Identities = 8/14 (57%), Positives = 9/14 (64%), Gaps = 1/14 (7%)

Query: 67  ARGP-LVGNPWHRA 79
           A GP LV +PW R 
Sbjct: 192 AHGPRLVADPWSRE 205


>gnl|CDD|217660 pfam03653, UPF0093, Uncharacterized protein family (UPF0093). 
          Length = 147

 Score = 26.0 bits (58), Expect = 2.4
 Identities = 6/21 (28%), Positives = 8/21 (38%)

Query: 23 YHIEVNPNDAGIYDRVVVMEL 43
          YH E  P      +   +ME 
Sbjct: 32 YHAEAAPGSDESDEIFKIMER 52


>gnl|CDD|214349 CHL00060, atpB, ATP synthase CF1 beta subunit.
          Length = 494

 Score = 25.8 bits (57), Expect = 3.1
 Identities = 9/18 (50%), Positives = 14/18 (77%)

Query: 32  AGIYDRVVVMELIKNVAQ 49
           AG+   V++MELI N+A+
Sbjct: 170 AGVGKTVLIMELINNIAK 187


>gnl|CDD|184791 PRK14686, PRK14686, hypothetical protein; Provisional.
          Length = 119

 Score = 25.5 bits (56), Expect = 3.1
 Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 2/39 (5%)

Query: 12  KKIDIMTTASNYHIEVNPNDAGIYDRVVVMELIKNVAQT 50
           KKI ++  A N++IE    D  I  R  ++ ++KN A  
Sbjct: 71  KKIQLLVKAVNHYIEDKDLDVEI--RFDIIAIVKNKAGF 107


>gnl|CDD|211621 TIGR01039, atpD, ATP synthase, F1 beta subunit.  The sequences of
           ATP synthase F1 alpha and beta subunits are related and
           both contain a nucleotide-binding site for ATP and ADP.
           They have a common amino terminal domain but vary at the
           C-terminus. The beta chain has catalytic activity, while
           the alpha chain is a regulatory subunit. Proton
           translocating ATP synthase, F1 beta subunit is
           homologous to proton translocating ATP synthase
           archaeal/vacuolar(V1), A subunit [Energy metabolism,
           ATP-proton motive force interconversion].
          Length = 461

 Score = 25.4 bits (56), Expect = 4.0
 Identities = 8/18 (44%), Positives = 13/18 (72%)

Query: 32  AGIYDRVVVMELIKNVAQ 49
           AG+   V++ ELI N+A+
Sbjct: 152 AGVGKTVLIQELINNIAK 169


>gnl|CDD|223133 COG0055, AtpD, F0F1-type ATP synthase, beta subunit [Energy
           production and conversion].
          Length = 468

 Score = 25.3 bits (56), Expect = 4.3
 Identities = 8/18 (44%), Positives = 13/18 (72%)

Query: 32  AGIYDRVVVMELIKNVAQ 49
           AG+   V++ ELI N+A+
Sbjct: 156 AGVGKTVLIQELINNIAK 173


>gnl|CDD|238553 cd01133, F1-ATPase_beta, F1 ATP synthase beta subunit,
          nucleotide-binding domain. The F-ATPase is found in
          bacterial plasma membranes, mitochondrial inner
          membranes and in chloroplast thylakoid membranes. It
          has also been found in the archaea Methanosarcina
          barkeri. It uses a proton gradient to drive ATP
          synthesis and hydrolyzes ATP to build the proton
          gradient. The extrinisic membrane domain, F1,  is
          composed of alpha, beta, gamma, delta and epsilon
          subunits with a stoichiometry of 3:3:1:1:1. The beta
          subunit of ATP synthase is catalytic.
          Length = 274

 Score = 25.3 bits (56), Expect = 4.4
 Identities = 9/18 (50%), Positives = 14/18 (77%)

Query: 32 AGIYDRVVVMELIKNVAQ 49
          AG+   V++MELI N+A+
Sbjct: 78 AGVGKTVLIMELINNIAK 95


>gnl|CDD|236447 PRK09280, PRK09280, F0F1 ATP synthase subunit beta; Validated.
          Length = 463

 Score = 25.1 bits (56), Expect = 4.6
 Identities = 8/18 (44%), Positives = 13/18 (72%)

Query: 32  AGIYDRVVVMELIKNVAQ 49
           AG+   V++ ELI N+A+
Sbjct: 153 AGVGKTVLIQELINNIAK 170


>gnl|CDD|238906 cd01925, cyclophilin_CeCYP16-like, cyclophilin_CeCYP16-like:
          cyclophilin-type peptidylprolyl cis- trans isomerase)
          (PPIase) domain similar to Caenorhabditis elegans
          cyclophilin 16. C. elegans CeCYP-16, compared to the
          archetypal cyclophilin Human cyclophilin A has, a
          reduced peptidylprolyl cis- trans isomerase activity,
          is cyclosporin insensitive and shows an altered
          substrate preference favoring, hydrophobic, acidic or
          amide amino acids. Most members of this subfamily have
          a glutamate residue in the active site at the position
          equivalent to a tryptophan (W121 in Human cyclophilin
          A), which has been shown to be important for
          cyclophilin binding.
          Length = 171

 Score = 25.0 bits (55), Expect = 5.7
 Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 16/63 (25%)

Query: 9  PSKKKIDIMTTASNYHIEVNPNDA-------------GIYDRVVVMELIKN-VAQTNQLD 54
          P+  K+ + TTA +  IE+   +A             G YD  +   ++   + Q    D
Sbjct: 3  PTTGKVILKTTAGDIDIELWSKEAPKACRNFIQLCLEGYYDNTIFHRVVPGFIIQGG--D 60

Query: 55 PNG 57
          P G
Sbjct: 61 PTG 63


  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
   0.314    0.132    0.381 

Gapped
Lambda     K      H
   0.267   0.0809    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,201,675
Number of extensions: 331122
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 179
Number of HSP's successfully gapped: 14
Length of query: 85
Length of database: 10,937,602
Length adjustment: 53
Effective length of query: 32
Effective length of database: 8,586,840
Effective search space: 274778880
Effective search space used: 274778880
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: 42 (22.0 bits)
S2: 53 (24.0 bits)