RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9435
         (106 letters)



>gnl|CDD|239579 cd03499, SQR_TypeC_SdhC, Succinate:quinone oxidoreductase (SQR)
          Type C subfamily, Succinate dehydrogenase C (SdhC)
          subunit; composed of bacterial SdhC and eukaryotic
          large cytochrome b binding (CybL) proteins. SQR
          catalyzes the oxidation of succinate to fumarate
          coupled to the reduction of quinone to quinol. Members
          of this family reduce high potential quinones such as
          ubiquinone. SQR is also called succinate dehydrogenase
          or Complex II, and is part of the citric acid cycle and
          the aerobic respiratory chain.  SQR is composed of a
          flavoprotein catalytic subunit, an iron-sulfur protein
          and one or two hydrophobic transmembrane subunits.
          Proteins in this subfamily are classified as Type C
          SQRs because they contain two transmembrane subunits
          and one heme group. The heme and quinone binding sites
          reside in the transmembrane subunits. The SdhC or CybL
          protein is one of the  two transmembrane subunits of
          bacterial and eukaryotic SQRs. The two-electron
          oxidation of succinate in the flavoprotein active site
          is coupled to the two-electron reduction of quinone in
          the membrane anchor subunits via electron transport
          through FAD and three iron-sulfur centers. The
          reversible reduction of quinone is an essential feature
          of respiration, allowing transfer of electrons between
          respiratory complexes.
          Length = 117

 Score = 61.0 bits (149), Expect = 1e-13
 Identities = 22/37 (59%), Positives = 26/37 (70%)

Query: 54 RPLSPHLTIYKLQITSVLSITHRGTGVALTAYALGLA 90
          RPLSPHLTIY+  +T++LSI HR TGVAL      L 
Sbjct: 1  RPLSPHLTIYRPPLTAILSILHRITGVALFLGLPLLL 37


>gnl|CDD|234076 TIGR02970, succ_dehyd_cytB, succinate dehydrogenase, cytochrome
          b556 subunit.  In E. coli and many other bacteria, two
          small, hydrophobic, mutually homologous subunits of
          succinate dehydrogenase, a TCA cycle enzyme, are SdhC
          and SdhD. This family is the SdhC, the cytochrome b
          subunit, called b556 in bacteria and b560 in
          mitochondria. SdhD (see TIGR02968) is called the
          hydrophobic membrane anchor subunit, although both SdhC
          and SdhD participate in anchoring the complex. In some
          bacteria, this cytochrome b subunit is replaced my a
          member of the cytochrome b558 family (see TIGR02046)
          [Energy metabolism, TCA cycle].
          Length = 120

 Score = 53.3 bits (129), Expect = 1e-10
 Identities = 21/37 (56%), Positives = 24/37 (64%)

Query: 54 RPLSPHLTIYKLQITSVLSITHRGTGVALTAYALGLA 90
          RPLSPHL IY+  IT++LSI HR TGV L      L 
Sbjct: 3  RPLSPHLQIYRFPITAILSILHRITGVLLFFGLPFLL 39


>gnl|CDD|216313 pfam01127, Sdh_cyt, Succinate dehydrogenase/Fumarate reductase
          transmembrane subunit.  This family includes a
          transmembrane protein from both the Succinate
          dehydrogenase and Fumarate reductase complexes.
          Length = 123

 Score = 50.1 bits (120), Expect = 3e-09
 Identities = 21/44 (47%), Positives = 27/44 (61%)

Query: 51 RLGRPLSPHLTIYKLQITSVLSITHRGTGVALTAYALGLAGVGL 94
          R  RPLSPHL +Y+  + ++LSI HR TGVAL    + L    L
Sbjct: 2  RKNRPLSPHLGLYRAHLGTILSILHRITGVALAVLLIHLLLWLL 45


>gnl|CDD|224920 COG2009, SdhC, Succinate dehydrogenase/fumarate reductase,
          cytochrome b subunit [Energy production and
          conversion].
          Length = 132

 Score = 44.3 bits (105), Expect = 6e-07
 Identities = 17/32 (53%), Positives = 21/32 (65%)

Query: 54 RPLSPHLTIYKLQITSVLSITHRGTGVALTAY 85
          RP+SPHL IY+  IT   SI HR +GV L  +
Sbjct: 3  RPVSPHLQIYRPPITMYASILHRISGVILAFF 34


>gnl|CDD|177741 PLN00130, PLN00130, succinate dehydrogenase (SDH3); Provisional.
          Length = 213

 Score = 39.0 bits (90), Expect = 1e-04
 Identities = 23/52 (44%), Positives = 33/52 (63%), Gaps = 2/52 (3%)

Query: 54  RPLSPHLTIYKLQITSVLSITHRGTGVALTAYALGLAGVGLTTDINSVVPTY 105
           RPLSPHL++Y+ Q+ S+LSI +R +GV LT   +  AG  L   +  +  TY
Sbjct: 125 RPLSPHLSVYQPQMNSMLSIFNRISGVYLT--GVTFAGYLLYLKMGMICLTY 174


>gnl|CDD|177738 PLN00127, PLN00127, succinate dehydrogenase (ubiquinone)
          cytochrome b subunit; Provisional.
          Length = 178

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 7/49 (14%)

Query: 53 GRPLSPHL-------TIYKLQITSVLSITHRGTGVALTAYALGLAGVGL 94
           RPLSP +       T YK  + ++ SIT+R TG  L+  A G   + L
Sbjct: 51 KRPLSPDVMDIDGKSTHYKFPVVALSSITNRVTGCVLSGGAAGGGVLAL 99


>gnl|CDD|165695 PLN00126, PLN00126, succinate dehydrogenase, cytochrome b subunit
           family; Provisional.
          Length = 129

 Score = 35.9 bits (82), Expect = 0.001
 Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 30  IKPVAAPTGV-PSKEGHAVRNERLGRPLSPHLTIYKLQITSVLSITHRGTGVALTA 84
            +P  +P+G  P      +      RPLSPHL + K Q+++  SI+HR  G AL A
Sbjct: 57  QRPKMSPSGSRPLHTSRPLSAPVANRPLSPHLPLKKPQLSATFSISHRIFGAALGA 112


>gnl|CDD|165700 PLN00131, PLN00131, hypothetical protein; Provisional.
          Length = 218

 Score = 34.2 bits (78), Expect = 0.005
 Identities = 15/23 (65%), Positives = 16/23 (69%)

Query: 54 RPLSPHLTIYKLQITSVLSITHR 76
          RPLSPHL IYK Q+TS   I  R
Sbjct: 5  RPLSPHLPIYKPQLTSAFPIFRR 27


>gnl|CDD|224222 COG1303, COG1303, Uncharacterized protein conserved in archaea
          [Function unknown].
          Length = 179

 Score = 29.2 bits (66), Expect = 0.26
 Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 7/35 (20%)

Query: 70 VLSITHRG-------TGVALTAYALGLAGVGLTTD 97
          VL + HR        T VALTA A G  G+ L  +
Sbjct: 6  VLRLGHRPERDKRITTHVALTARAFGADGILLDGE 40


>gnl|CDD|235181 PRK03958, PRK03958, tRNA 2'-O-methylase; Reviewed.
          Length = 176

 Score = 28.0 bits (63), Expect = 0.72
 Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 7/42 (16%)

Query: 70  VLSITHRG-------TGVALTAYALGLAGVGLTTDINSVVPT 104
           VL + HR        T V LTA ALG   + L ++   V  +
Sbjct: 5   VLRLGHRPERDKRITTHVGLTARALGADKIILASNDEHVKES 46


>gnl|CDD|176138 cd08447, PBP2_LTTR_aromatics_like_1, The C-terminal substrate
           binding domain of an uncharacterized LysR-type
           transcriptional regulator similar to regulators involved
           in the catabolism of aromatic compounds, contains type 2
           periplasmic binding fold.  This CD represents the
           substrate binding domain of an uncharacterized LysR-type
           regulator similar to CbnR which is involved in the
           regulation of chlorocatechol breakdown. The
           transcription of the genes encoding enzymes involved in
           such degradation is regulated and expression of these
           enzymes is enhanced by inducers, which are either an
           intermediate in the metabolic pathway or compounds to be
           degraded. This substrate-binding domain shows
           significant homology to the type 2 periplasmic binding
           proteins (PBP2), which are responsible for the uptake of
           a variety of substrates such as phosphate, sulfate,
           polysaccharides, lysine/arginine/ornithine, and
           histidine. The PBP2 bind their ligand in the cleft
           between these domains in a manner resembling a Venus
           flytrap. After binding their specific ligand with high
           affinity, they can interact with a cognate membrane
           transport complex comprised of two integral membrane
           domains and two cytoplasmically located ATPase domains.
           This interaction triggers the ligand translocation
           across the cytoplasmic membrane energized by ATP
           hydrolysis.
          Length = 198

 Score = 28.0 bits (63), Expect = 0.78
 Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 3/38 (7%)

Query: 58  PHLTIYKLQITSVLSITHRGTGVAL---TAYALGLAGV 92
           P    Y  QI ++L++   G GVAL   +A  L   GV
Sbjct: 126 PRYVQYLSQIHTMLALVRAGLGVALVPASASRLRFEGV 163


>gnl|CDD|181900 PRK09487, sdhC, succinate dehydrogenase cytochrome b556 large
          membrane subunit; Provisional.
          Length = 129

 Score = 27.0 bits (60), Expect = 1.2
 Identities = 16/42 (38%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 48 RNERLGRPLSPHLTIYKLQITSVLSITHRGTGVALTAYALGL 89
          RN +  RP++  L   +  IT++ SI HR +GV +T  A+G+
Sbjct: 3  RNVKKQRPVNLDLQTIRFPITAIASILHRVSGV-ITFVAVGI 43


>gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated.
          Length = 251

 Score = 25.8 bits (57), Expect = 4.2
 Identities = 11/27 (40%), Positives = 16/27 (59%)

Query: 24  HIRTITIKPVAAPTGVPSKEGHAVRNE 50
           ++R +T K VAA  G+  +E  A  NE
Sbjct: 122 YMRNVTPKEVAAELGMTEEEVEATMNE 148


>gnl|CDD|213989 cd07434, PHP_PolIIIA_DnaE2, Polymerase and Histidinol Phosphatase
           domain of alpha-subunit of bacterial polymerase III at
           DnaE2 gene.  PolIIIA DnaE2 plays a role in SOS
           mutagenesis/translesion synthesis and has dominant
           effects in determining GC variability in the bacterial
           genome. PolIIIAs that contain an N-terminal PHP domain
           have been classified into four basic groups based on
           genome composition, phylogenetic, and domain structural
           analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also
           called histidinol phosphatase-2/HIS2) domain is
           associated with several types of DNA polymerases, such
           as PolIIIA and family X DNA polymerases, stand alone
           histidinol phosphate phosphatases (HisPPases), and a
           number of uncharacterized protein families. DNA
           polymerase III holoenzyme is one of the five eubacterial
           DNA polymerases that are responsible for the replication
           of the DNA duplex. PolIIIA core enzyme catalyzes the
           reaction for polymerizing both DNA strands. PolC PHP is
           located in a different location compared to dnaE1, 2,
           and 3. dnaE1 is the longest compared to dnaE2 and dnaE3.
           A unique motif was also identified in dnaE1 and dnaE3
           genes. The PHP domain has four conserved sequence motifs
           and contains an invariant histidine that is involved in
           metal ion coordination. PHP domains found in DnaEs of
           thermophilic origin exhibit 3'-5' exonuclease activity.
          Length = 260

 Score = 25.5 bits (57), Expect = 5.1
 Identities = 6/19 (31%), Positives = 9/19 (47%), Gaps = 1/19 (5%)

Query: 83  TAYALGLAGVGLTTDINSV 101
            A  LG   + + TD  S+
Sbjct: 25  RAAELGYRALAI-TDECSL 42


  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    0.135    0.392 

Gapped
Lambda     K      H
   0.267   0.0767    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,224,200
Number of extensions: 438468
Number of successful extensions: 418
Number of sequences better than 10.0: 1
Number of HSP's gapped: 417
Number of HSP's successfully gapped: 30
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
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)