RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4837
         (100 letters)



>gnl|CDD|218089 pfam04442, CtaG_Cox11, Cytochrome c oxidase assembly protein
           CtaG/Cox11.  Cytochrome c oxidase assembly protein is
           essential for the assembly of functional cytochrome
           oxidase protein. In eukaryotes it is an integral protein
           of the mitochondrial inner membrane. Cox11 is essential
           for the insertion of Cu(I) ions to form the CuB site.
           This is essential for the stability of other structures
           in subunit I, for example haems a and a3, and the
           magnesium/manganese centre. Cox11 is probably only
           required in sub-stoichiometric amounts relative to the
           structural units. The C terminal region of the protein
           is known to form a dimer. Each monomer coordinates one
           Cu(I) ion via three conserved cysteine residues (111,
           208 and 210) in Saccharomyces cerevisiae. Met 224 is
           also thought to play a role in copper transfer or
           stabilising the copper site.
          Length = 150

 Score =  113 bits (285), Expect = 8e-34
 Identities = 36/58 (62%), Positives = 45/58 (77%)

Query: 13  VYPGETALAFYTAKNPTNSPIVGISTYNVVPFDAGQYFNKIQCFCFEEQQLNPHEELQ 70
           V+PGETALAFY AKNP++ PIVG +  +V P  AG YFNKI+CFCF +Q L P EE++
Sbjct: 62  VHPGETALAFYEAKNPSDRPIVGQAVPSVTPGQAGAYFNKIECFCFTQQTLQPGEEVE 119


>gnl|CDD|185464 PTZ00128, PTZ00128, cytochrome c oxidase assembly protein-like;
           Provisional.
          Length = 232

 Score =  115 bits (290), Expect = 1e-33
 Identities = 39/59 (66%), Positives = 51/59 (86%)

Query: 13  VYPGETALAFYTAKNPTNSPIVGISTYNVVPFDAGQYFNKIQCFCFEEQQLNPHEELQI 71
           V PGETALAFY AKN ++ P++G++TY++ P +AG YFNKIQCFCFEEQ+LNPHEE+ +
Sbjct: 134 VLPGETALAFYRAKNRSDKPVIGVATYHIAPPEAGLYFNKIQCFCFEEQRLNPHEEVDM 192


>gnl|CDD|235341 PRK05089, PRK05089, cytochrome C oxidase assembly protein;
           Provisional.
          Length = 188

 Score = 96.1 bits (240), Expect = 2e-26
 Identities = 30/61 (49%), Positives = 41/61 (67%)

Query: 10  TLHVYPGETALAFYTAKNPTNSPIVGISTYNVVPFDAGQYFNKIQCFCFEEQQLNPHEEL 69
           ++ V+PGE  L FY A+N ++ PIVG +  +V P  AG YFNKI+CFCF +Q L P E  
Sbjct: 87  SVDVHPGELNLVFYEAENLSDRPIVGQAIPSVTPGQAGAYFNKIECFCFTQQTLQPGETR 146

Query: 70  Q 70
           +
Sbjct: 147 E 147


>gnl|CDD|225716 COG3175, COX11, Cytochrome oxidase assembly factor
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 195

 Score = 95.6 bits (238), Expect = 3e-26
 Identities = 33/59 (55%), Positives = 42/59 (71%)

Query: 11  LHVYPGETALAFYTAKNPTNSPIVGISTYNVVPFDAGQYFNKIQCFCFEEQQLNPHEEL 69
           ++V PGET L FY A+N ++ PI G +TYNV P  AG YFNK++CFCF EQ L P E +
Sbjct: 87  VYVRPGETNLIFYEAENLSDKPITGQATYNVAPGQAGAYFNKVECFCFTEQTLKPGETV 145


>gnl|CDD|235301 PRK04452, PRK04452, acetyl-CoA decarbonylase/synthase complex
          subunit delta; Provisional.
          Length = 319

 Score = 28.7 bits (65), Expect = 0.36
 Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 1/31 (3%)

Query: 16 GETALAFYTAKNPT-NSPIVGISTYNVVPFD 45
          GETAL FY  + P  N P++ +  +++ P D
Sbjct: 31 GETALPFYHFEGPMPNPPVIAMEVFDMPPED 61


>gnl|CDD|223739 COG0667, Tas, Predicted oxidoreductases (related to aryl-alcohol
           dehydrogenases) [Energy production and conversion].
          Length = 316

 Score = 28.4 bits (64), Expect = 0.58
 Identities = 11/24 (45%), Positives = 14/24 (58%)

Query: 15  PGETALAFYTAKNPTNSPIVGIST 38
           P + ALA+  A+    SPIVG S 
Sbjct: 258 PAQVALAWVLAQPGVTSPIVGASK 281


>gnl|CDD|234463 TIGR04089, exp_by_SipW_III, alternate signal-mediated exported
          protein, RER_14450 family.  Members of this
          Actinobacterial protein family contain the cognate
          signal peptide domain, modeled by TIGR04088, for the
          variant SipW form of the signal peptidase I family. The
          remainder of this protein, however, differs from
          families such as Peptidase_M73 (pfam12389) and YqxM
          (TIGR04087) that share the same signal peptide domain.
          Some additional homologs to this family lack
          full-length homology and are excluded by the trusted
          cutoff as set. The two known targets for export by the
          SipW signal peptidase in Bacillus subtilis act in
          producing biofilm matrix material.
          Length = 179

 Score = 26.6 bits (59), Expect = 2.0
 Identities = 7/34 (20%), Positives = 13/34 (38%)

Query: 16 GETALAFYTAKNPTNSPIVGISTYNVVPFDAGQY 49
                 +       + ++ I+TY +VP D   Y
Sbjct: 47 SAATGGGWKDVTGAGAVVIDIATYKIVPGDTLTY 80


>gnl|CDD|178050 PLN02431, PLN02431, ferredoxin--nitrite reductase.
          Length = 587

 Score = 26.3 bits (58), Expect = 3.2
 Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 2/40 (5%)

Query: 26  KNPTNSPIVGISTYNVVPFDAGQYFNKIQCFCFEEQQLNP 65
           +NP  +P+ GI  + +V  D   Y N +  +     + NP
Sbjct: 210 RNPVGNPLAGIDPHEIV--DTRPYTNLLSDYITNNGRGNP 247


>gnl|CDD|131680 TIGR02632, RhaD_aldol-ADH, rhamnulose-1-phosphate aldolase/alcohol
           dehydrogenase. 
          Length = 676

 Score = 25.6 bits (56), Expect = 4.9
 Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 4/42 (9%)

Query: 6   RYLLTLHVYPGETALAFYTAKNPTNSPIVGISTYNVVPFDAG 47
           R LL  H++P + A A +   +  +      +T  ++  D G
Sbjct: 632 RTLLKRHIFPADIAEAVFFLASSKSEK----TTGCIITVDGG 669


>gnl|CDD|177878 PLN02234, PLN02234, 1-deoxy-D-xylulose-5-phosphate synthase.
          Length = 641

 Score = 25.8 bits (56), Expect = 5.4
 Identities = 14/42 (33%), Positives = 21/42 (50%)

Query: 16  GETALAFYTAKNPTNSPIVGISTYNVVPFDAGQYFNKIQCFC 57
           G T L  + ++ PT    VGI+  + V F AG     ++ FC
Sbjct: 386 GGTMLNLFESRFPTRCFDVGIAEQHAVTFAAGLACEGLKPFC 427


>gnl|CDD|212507 cd11648, RsmI, Ribosomal RNA small subunit methyltransferase I,
          also known as rRNA (cytidine-2'-O-)-methyltransferase
          RsmI.  Proteins in this family catalyze the
          2-O-methylation of the ribose of cytidine 1402 (C1402)
          in 16S rRNA using S-adenosyl-L-methionine (SAM or
          Ado-Met) as the methyl donor. RsmI proteins employ the
          30S subunit (not the 16S rRNA) as a substrate,
          suggesting that the methylation reaction occurs at a
          late step during 30S assembly in the cell.
          Length = 218

 Score = 25.4 bits (57), Expect = 6.0
 Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 9/39 (23%)

Query: 69 LQIFAPKKP-----HHNEHKMRSQILPKVE----IANVS 98
          L  +  KKP      HNE +   +I+ +++    +A VS
Sbjct: 40 LNHYGIKKPLISYHEHNEEERAEEIIERLKEGKSVALVS 78


>gnl|CDD|178455 PLN02864, PLN02864, enoyl-CoA hydratase.
          Length = 310

 Score = 25.1 bits (55), Expect = 8.5
 Identities = 10/13 (76%), Positives = 11/13 (84%), Gaps = 2/13 (15%)

Query: 6   RYLLTLHVYPGET 18
           R+LL  HVYPGET
Sbjct: 261 RFLL--HVYPGET 271


  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
   0.320    0.134    0.408 

Gapped
Lambda     K      H
   0.267   0.0802    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,960,629
Number of extensions: 394875
Number of successful extensions: 255
Number of sequences better than 10.0: 1
Number of HSP's gapped: 255
Number of HSP's successfully gapped: 17
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.1 bits)