RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8730
         (287 letters)



>gnl|CDD|218469 pfam05154, TM2, TM2 domain.  This family is composed of a pair of
          transmembrane alpha helices connected by a short
          linker. The function of this domain is unknown, however
          it occurs in a wide range or protein contexts.
          Length = 51

 Score = 64.9 bits (159), Expect = 5e-14
 Identities = 23/50 (46%), Positives = 27/50 (54%)

Query: 29 EKSLYITYLLWLVGGIFGVHHFYLGRDIQGFLWWCTLGGYFGFGWLRDIF 78
          +KS  I  LL L  G FGVH FYLG+   G L+  T  G  G  WL D+ 
Sbjct: 2  KKSKLIALLLSLFLGGFGVHRFYLGKTGTGILYLLTFWGILGIWWLIDLI 51


>gnl|CDD|222840 PHA01886, PHA01886, TM2 domain-containing protein.
          Length = 78

 Score = 48.4 bits (115), Expect = 8e-08
 Identities = 26/59 (44%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 30 KSLYITYLLWLVGGIFGVHHFYLGRDIQGFLWWCTLGGYFGFGWLRDIFHIQNYVADAN 88
          KS  I Y+LW   G FG+H FY G    G +W  T GG FG GW  D+F     V  +N
Sbjct: 2  KSTAIAYVLWFFLGFFGIHRFYTGNIATGIIWLFT-GGLFGIGWFIDLFLTAGLVQSSN 59


>gnl|CDD|225196 COG2314, XynA, Predicted membrane protein [Function unknown].
          Length = 95

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 5/65 (7%)

Query: 33 YITYLLWLVGGIFGVHHFYLGRDIQGFLWWCTLGGYFGFGWLRDIFHIQNYVADANKDRD 92
           I  LL  + GIFG+H FYLG+  +G L           G    +  I  Y+     D  
Sbjct: 11 LIAGLLAALFGIFGLHKFYLGQGGKGIL----TLLLNWTGIFLILLLI-GYLGVLLGDEF 65

Query: 93 YLDKF 97
          Y+D  
Sbjct: 66 YIDGI 70


>gnl|CDD|227826 COG5539, COG5539, Predicted cysteine protease (OTU family)
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 306

 Score = 35.6 bits (82), Expect = 0.022
 Identities = 27/124 (21%), Positives = 42/124 (33%), Gaps = 21/124 (16%)

Query: 19  NNSDKTKVHAEKSLYITYLLWLVGGIFGVHHFYLGRDIQGFLWWCTLGGYFGFGWLRDIF 78
           +N D       +   I Y  W+V             D QG        G      + D  
Sbjct: 150 SNPDLYNPAILEIDVIAYATWIVK-----------PDSQG-------DGCIEIAIISDQL 191

Query: 79  HIQNYVADANKDRDYLDKFN-HNLRSYKYPPFSTIRFTGMTVVAYLWSTVVSMAIPEEDI 137
            ++ +V D +KD    D++N H         F+ I F   T+   LW T V+  + +   
Sbjct: 192 PVRIHVVDVDKDS--EDRYNSHPYVQRISILFTGIHFDEETLAMVLWDTYVNEVLFDASD 249

Query: 138 GGLP 141
           G   
Sbjct: 250 GITI 253


>gnl|CDD|179382 PRK02195, PRK02195, V-type ATP synthase subunit D; Provisional.
          Length = 201

 Score = 31.4 bits (72), Expect = 0.31
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 17/62 (27%)

Query: 235 YSSLWGSYLYFNA---KITDGE-------GEEIPLNEAI------HHFFKSPWWVDLLAV 278
           + SL+   LYF+    K+   E       G E+P+ ++I      +    +P WVD   +
Sbjct: 64  WISLFSEPLYFDEDLIKVKKVEKDYENIAGVEVPILDSIEFEIIEYSLLNTPIWVD-TGI 122

Query: 279 EL 280
           EL
Sbjct: 123 EL 124


>gnl|CDD|240601 cd12918, VKOR_arc, Vitamin K epoxide reductase family in archaea
           and some bacteria.  This family includes vitamin K
           epoxide reductase (VKOR) mostly present in archaea and
           some bacteria. VKOR (also named VKORC1) is an integral
           membrane protein that catalyzes the reduction of vitamin
           K 2,3-epoxide and vitamin K to vitamin K hydroquinone,
           an essential co-factor subsequently used in the
           gamma-carboxylation of glutamic acid residues in blood
           coagulation enzymes. All homologs of VKOR contain an
           active site CXXC motif, which is switched between
           reduced and disulfide-bonded states during the reaction
           cycle. In some bacterial homologs, the VKOR domain is
           fused with domains of the thioredoxin family of
           oxidoreductases which may function as redox partners in
           initiating the reduction cascade.
          Length = 126

 Score = 28.8 bits (65), Expect = 1.4
 Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 5/63 (7%)

Query: 125 STVVSMAIPEEDIGGLPWKYL---HFLLPIACALGVWSVGNIGHETGTIWWCLAAAYACY 181
             V+S   P   I G+P   L    F + +  +L       +       W  L  A+  Y
Sbjct: 39  EKVLS--SPYSRILGVPLAVLGLAWFAVLLVLSLLAALRVRLLLGALLYWSILGIAFVPY 96

Query: 182 PVY 184
            VY
Sbjct: 97  LVY 99


>gnl|CDD|236157 PRK08126, PRK08126, hypothetical protein; Provisional.
          Length = 432

 Score = 29.3 bits (66), Expect = 2.3
 Identities = 13/42 (30%), Positives = 16/42 (38%), Gaps = 3/42 (7%)

Query: 206 TLSKRWQTKPKPRKRFLRRC---LTIGACALLYSSLWGSYLY 244
            LS  WQ     R R  R      T    +L+   L+G Y Y
Sbjct: 224 ALSPHWQGAEPGRLRSFRDVPVWATAAVLSLILLGLFGWYKY 265


>gnl|CDD|132348 TIGR03305, alt_F1F0_F1_bet, alternate F1F0 ATPase, F1 subunit beta.
            A small number of taxonomically diverse prokaryotic
           species have what appears to be a second ATP synthase,
           in addition to the normal F1F0 ATPase in bacteria and
           A1A0 ATPase in archaea. These enzymes use ion gradients
           to synthesize ATP, and in principle may run in either
           direction. This model represents the F1 beta subunit of
           this apparent second ATP synthase.
          Length = 449

 Score = 29.4 bits (66), Expect = 2.5
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 8/75 (10%)

Query: 43  GIFGVHHFYLGRDIQGFLWWCTLGGYFGFGWLRDIFHIQNYVADANKDRDYLDKFNHNLR 102
           GI G  H+ L R+++      TL  Y     L+DI  +      + +DR  +++     R
Sbjct: 344 GIVGERHYDLAREVRQ-----TLAQY---EELKDIIAMLGLEQLSREDRRVVNRARRLER 395

Query: 103 SYKYPPFSTIRFTGM 117
               P F+T +FTGM
Sbjct: 396 FLTQPFFTTEQFTGM 410


>gnl|CDD|226582 COG4097, COG4097, Predicted ferric reductase [Inorganic ion
           transport and metabolism].
          Length = 438

 Score = 28.2 bits (63), Expect = 5.9
 Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 10/49 (20%)

Query: 109 FSTIRFTGMTVVAYLWSTVVSMAIPEEDIGGLPWKYLHFLLPIACALGV 157
           +S   F G+ +V  LW       I  E      W+  H L+ +   LG+
Sbjct: 132 WSAYIFIGLLLVWRLWL-----NIGYE-----NWRIAHRLMAVVYILGL 170


>gnl|CDD|238545 cd01125, repA, Hexameric Replicative Helicase RepA.  RepA is
           encoded by a plasmid, which is found in most Gram
           negative bacteria. RepA is a 5'-3' DNA helicase which
           can utilize ATP, GTP and CTP to a lesser extent.
          Length = 239

 Score = 27.4 bits (61), Expect = 8.7
 Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 3/41 (7%)

Query: 229 GACALLYSSLWGSYLYFNAKITDGEGEEIPLNEAIHHFFKS 269
           GA AL+  + W   L    ++T  E E++ + +A    F  
Sbjct: 174 GASALVDGARWVRAL---TRMTSEEAEKMGVGKAQPGLFFR 211


  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
   0.325    0.140    0.480 

Gapped
Lambda     K      H
   0.267   0.0674    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,094,550
Number of extensions: 1447492
Number of successful extensions: 1794
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1789
Number of HSP's successfully gapped: 37
Length of query: 287
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 191
Effective length of database: 6,679,618
Effective search space: 1275807038
Effective search space used: 1275807038
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.2 bits)