RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780543|ref|YP_003064956.1| NADH dehydrogenase [Candidatus
Liberibacter asiaticus str. psy62]
         (131 letters)



>gnl|CDD|147317 pfam05071, NDUFA12, NADH ubiquinone oxidoreductase subunit NDUFA12.
            This family contains the 17.2 kD subunit of complex I
           (NDUFA12) and its homologues. The family also contains a
           second related eukaryotic protein of unknown function.
          Length = 100

 Score =  105 bits (263), Expect = 6e-24
 Identities = 44/100 (44%), Positives = 56/100 (56%), Gaps = 3/100 (3%)

Query: 30  VGKDEFGNTYYESRKNINGSSRRWVIYNGYTDPSSIPPMWHGWIHHRRIGVPKAEEENSF 89
           VG+DEFGN YYE++  + G  RRWVIYNG  + S +PP WHGW+HH     P  E     
Sbjct: 4   VGEDEFGNKYYENKDEL-GGRRRWVIYNGKAEASRVPPEWHGWLHHTTDEPPTEEPLKPR 62

Query: 90  DWQKPHCVNATGSLNSYYPRFRRDNMAGTSTKGKYSAWSP 129
            W+KPH  N TG+  +Y P      +      G Y AW+P
Sbjct: 63  AWEKPHQPNLTGTPGAYRP--YGSLLRRPRATGDYEAWTP 100


>gnl|CDD|33556 COG3761, COG3761, NADH:ubiquinone oxidoreductase 17.2 kD subunit
           [Energy production and conversion].
          Length = 118

 Score =  102 bits (256), Expect = 2e-23
 Identities = 61/123 (49%), Positives = 74/123 (60%), Gaps = 8/123 (6%)

Query: 9   FTWWNGQTLGTRFFTWRFGHIVGKDEFGNTYYESR-KNINGSSRRWVIYNGYTDPSSIPP 67
           FTWWN QT GTRF        VG+DEFGN YYE R  +  G +RRWVIYNGY + S IPP
Sbjct: 1   FTWWN-QTFGTRFHK-----KVGEDEFGNVYYEGRNIDSEGRTRRWVIYNGYAEASKIPP 54

Query: 68  MWHGWIHHRRIGVPKAEEENSFDWQKPHCVNATGSLNSYYPRFR-RDNMAGTSTKGKYSA 126
            WHGW+HHR    PK+E+    +WQKPH  N TG+ ++Y P+             G Y A
Sbjct: 55  GWHGWLHHRVDEPPKSEQLFPREWQKPHLPNLTGTPHAYRPKGSLARAGERPRVTGDYDA 114

Query: 127 WSP 129
           W+P
Sbjct: 115 WTP 117


>gnl|CDD|38592 KOG3382, KOG3382, KOG3382, NADH:ubiquinone oxidoreductase, B17.2
           subunit [Energy production and conversion].
          Length = 151

 Score = 52.4 bits (125), Expect = 4e-08
 Identities = 35/111 (31%), Positives = 48/111 (43%), Gaps = 15/111 (13%)

Query: 25  RFGHIVGKDEFGNTYYESRKNINGSSRRWVIY----NGYTDPSSIPPMWHGWIHHRRIGV 80
           + G +VG D+FGN YYE+     G  R WV Y    N   D S +P  WHGW+H      
Sbjct: 45  KIGTLVGVDKFGNKYYENNDYFYGRHR-WVEYASKVNWDYDASQVPAEWHGWLHFITDDP 103

Query: 81  PKAEEE-NSFDWQKPHCVNATGSL-NSYYPRFRRDNMAGTSTKGKYSAWSP 129
           P  +       W   H  N +G    +Y P         ++T+ K  +W P
Sbjct: 104 PDEKLPLPPKKWILEHKENFSGETGETYVP--------YSTTRTKIQSWVP 146


>gnl|CDD|33055 COG3243, PhaC, Poly(3-hydroxyalkanoate) synthetase [Lipid
           metabolism].
          Length = 445

 Score = 30.3 bits (68), Expect = 0.17
 Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 27  GHIVGK-DEFGNTYYESRKNINGSSRRWVIYNGYTDPSSIPPMWHGWIHHR 76
           GHI G  +  GN  Y+   N+   +  W+       P S  P W  W+ HR
Sbjct: 368 GHIAGVVNPPGNAKYQYWTNLPADAEAWLSGAK-EHPGSWWPHWQQWLEHR 417


>gnl|CDD|35052 COG5493, COG5493, Uncharacterized conserved protein containing a
           coiled-coil domain [Function unknown].
          Length = 231

 Score = 26.9 bits (59), Expect = 1.7
 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 5/45 (11%)

Query: 25  RFGHIVGKDEFGNTYYESRKNINGSSRRWVIYNG----YTDPSSI 65
           R+G I+ +D F     E  + +     RW+ Y+     Y  PS +
Sbjct: 110 RWG-ILSEDAFRQGVREILREVGYVVERWLYYDKEGHVYGHPSDV 153


>gnl|CDD|39884 KOG4686, KOG4686, KOG4686, Predicted sugar transporter
           [Carbohydrate transport and metabolism].
          Length = 459

 Score = 26.9 bits (59), Expect = 1.8
 Identities = 9/43 (20%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 38  TYYESRKNINGSSRRWVIYNGYTDPSSIPPMWHGWIHHRRIGV 80
             ++   NI   ++  ++Y+ Y+ P+ +   + G++  RR G+
Sbjct: 68  IDFKLDSNIE-YAKFTLLYSVYSWPNVVLCFFGGFLIDRRFGI 109


>gnl|CDD|144097 pfam00378, ECH, Enoyl-CoA hydratase/isomerase family.  This family
           contains a diverse set of enzymes including: Enoyl-CoA
           hydratase. Napthoate synthase. Carnitate racemase.
           3-hydoxybutyryl-CoA dehydratase. Dodecanoyl-CoA
           delta-isomerase.
          Length = 169

 Score = 26.1 bits (58), Expect = 3.2
 Identities = 7/22 (31%), Positives = 7/22 (31%)

Query: 64  SIPPMWHGWIHHRRIGVPKAEE 85
            IP         R IG   A E
Sbjct: 124 IIPGAGGTQRLPRIIGHSAALE 145


>gnl|CDD|73323 cd02756, MopB_Arsenite-Ox, Arsenite oxidase (Arsenite-Ox) oxidizes
           arsenite to the less toxic arsenate; it transfers the
           electrons obtained from the oxidation of arsenite
           towards the soluble periplasmic electron carriers
           cytochrome c and/or amicyanin.  Arsenite oxidase is a
           heterodimeric enzyme containing a large and a small
           subunit. The large catalytic subunit harbors the
           molybdopterin cofactor and the [3Fe-4S] cluster; and the
           small subunit belongs to the structural class of the
           Rieske proteins. The small subunit is not included in
           this alignment. Members of MopB_Arsenite-Ox CD belong to
           the molybdopterin_binding (MopB) superfamily of
           proteins..
          Length = 676

 Score = 24.9 bits (54), Expect = 6.1
 Identities = 16/83 (19%), Positives = 29/83 (34%), Gaps = 15/83 (18%)

Query: 22  FTWRFGHIVGKDEFGNTYYESRKNINGSSRRWVIYNGYTDP--SSIPPMW-HGWIHHR-- 76
                 H++          E+   +NG  RR  +Y  + DP   ++P  W    I +R  
Sbjct: 508 KLAEDAHVILPAAANGEMNETS--MNGHERRLRLYEKFMDPPGEAMPDWWIAAMIANRIY 565

Query: 77  -------RIGVPKAEEENSFDWQ 92
                  + G  + +    F W+
Sbjct: 566 ELYQEEGKGGSAQYQFFG-FIWK 587


>gnl|CDD|143625 cd07758, ThTPase, Thiamine Triphosphatase.  ThTPase is a soluble
          cytosolic enzyme which converts thiamine triphosphate
          (ThTP) to thiamine diphosphate. This catalytic activity
          depends on a divalent metal cofactor, for example Mg++.
          ThTPase regulates the intracellular concentration of
          ThTP, maintaining it at a low concentration in vivo.
          ThTP acts as a messenger in cell signaling in response
          to cellular stress, and in addition, can phosphorylate
          proteins in certain tissues. There is another class of
          membrane-associated enzymes in animal tissues which
          also convert ThTP to thiamine diphosphate, however they
          do not belong to this subgroup. This subgroup belongs
          to the CYTH/triphosphate tunnel metalloenzyme
          (TTM)-like superfamily, whose enzymes have a unique
          active site located within an eight-stranded beta
          barrel.
          Length = 196

 Score = 24.6 bits (54), Expect = 7.9
 Identities = 7/29 (24%), Positives = 15/29 (51%)

Query: 26 FGHIVGKDEFGNTYYESRKNINGSSRRWV 54
             ++G+  F +TYY++  N    +  W+
Sbjct: 23 LLELLGRRTFHDTYYDTPDNTLSLNDVWL 51


>gnl|CDD|109889 pfam00851, Peptidase_C6, Helper component proteinase.  This protein
           is found in genome polyproteins of potyviruses.
          Length = 453

 Score = 24.5 bits (54), Expect = 8.7
 Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 2/30 (6%)

Query: 20  RFFTWRFGHIVGKDEFGNTYYESRKNINGS 49
           RFF+  F  I   +  G + Y  RKN NG+
Sbjct: 213 RFFSNYFEEIDPSE--GYSKYIIRKNPNGT 240


>gnl|CDD|145580 pfam02516, STT3, Oligosaccharyl transferase STT3 subunit.  This
           family consists of the oligosaccharyl transferase STT3
           subunit and related proteins. The STT3 subunit is part
           of the oligosaccharyl transferase (OTase) complex of
           proteins and is required for its activity. OTase
           transfers a lipid-linked core-oligosaccharide to
           selected asparagine residues in the ER.
          Length = 650

 Score = 24.3 bits (53), Expect = 9.3
 Identities = 12/98 (12%), Positives = 30/98 (30%), Gaps = 22/98 (22%)

Query: 24  WRFGHIVGKDEFGNTYYESRKNINGSSRRWVIYNGYTDPSSIPPMWHGWIHHRRIGVPKA 83
           W +GH          Y+         + R V ++G + P  +      W           
Sbjct: 457 WDYGHFF-------AYF---------ADRPVTFDGGSSPVVLGTPRGYW-----ALTLMD 495

Query: 84  EEENSFDWQKPHCVNATGSLNSYY-PRFRRDNMAGTST 120
           +   ++     + +  T  + S++    +   +A  + 
Sbjct: 496 DNNEAYLSLGINSMLDTSGVKSWWDYGNQILKVAKRAV 533


>gnl|CDD|37592 KOG2381, KOG2381, KOG2381, Phosphatidylinositol 4-kinase [Signal
           transduction mechanisms].
          Length = 286

 Score = 24.5 bits (53), Expect = 9.7
 Identities = 8/30 (26%), Positives = 14/30 (46%)

Query: 57  NGYTDPSSIPPMWHGWIHHRRIGVPKAEEE 86
           +G   P   P  W  W++  +  +P +EE 
Sbjct: 184 HGLCFPEKHPDEWFEWLYWPQAKIPFSEEI 213


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.320    0.137    0.481 

Gapped
Lambda     K      H
   0.267   0.0752    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,878,584
Number of extensions: 93936
Number of successful extensions: 215
Number of sequences better than 10.0: 1
Number of HSP's gapped: 210
Number of HSP's successfully gapped: 16
Length of query: 131
Length of database: 6,263,737
Length adjustment: 83
Effective length of query: 48
Effective length of database: 4,470,190
Effective search space: 214569120
Effective search space used: 214569120
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 (21.8 bits)
S2: 52 (23.8 bits)