RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254781041|ref|YP_003065454.1| succinate dehydrogenase
protein, cytochrome b subunit [Candidatus Liberibacter asiaticus str.
psy62]
         (129 letters)



>gnl|CDD|163092 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).
          Length = 120

 Score =  111 bits (281), Expect = 4e-26
 Identities = 39/120 (32%), Positives = 72/120 (60%)

Query: 6   NNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRCYMD 65
             RPLSPHLQIYR   T  +SI+HRITG +++ G P +++W     +   + +++   + 
Sbjct: 1   KQRPLSPHLQIYRFPITAILSILHRITGVLLFFGLPFLLWWLSLSLSSPESFATVHALLS 60

Query: 66  GSVFEVCLFLYTWAVIHHMLGGIRYLIWDVSLCLDKKIATQMAKINIIASILTVLIVWII 125
             + ++ L+   WA+++H+L GIR+L+WD+   L+ K A   A + ++ S++  ++  I 
Sbjct: 61  SPLGKLILWGLLWALLYHLLAGIRHLLWDLGYGLELKSARISAWVVLVLSLVLTILAGIW 120


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

 Score = 46.4 bits (110), Expect = 2e-06
 Identities = 26/100 (26%), Positives = 43/100 (43%), Gaps = 12/100 (12%)

Query: 5   KNNRPLSPHLQ-------IYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANG-EHT 56
              RPLSP +         Y+       SI +R+TG V+  G          +  G E  
Sbjct: 49  LEKRPLSPDVMDIDGKSTHYKFPVVALSSITNRVTGCVLSGG--AAGGGVLALVGGSEAV 106

Query: 57  LSSLRCYMDGSVFEV--CLFLYTWAVIHHMLGGIRYLIWD 94
            +++  +  G    V    F  ++  ++H LGG+R+L+WD
Sbjct: 107 PATMEGFKSGGPLIVFPAKFAVSFPFVYHTLGGLRHLVWD 146


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

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 29/126 (23%), Positives = 60/126 (47%), Gaps = 5/126 (3%)

Query: 3   SIKNNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVVVFWFFCIANGEHTLSSLRC 62
           ++K  RP++  LQ  R   T   SI+HR++G + ++   ++++      +          
Sbjct: 4   NVKKQRPVNLDLQTIRFPITAIASILHRVSGVITFVAVGILLWLLGTSLSSPEGFEQAAA 63

Query: 63  YMDGSVFEVCLFLYTWAVIHHMLGGIRYLIWDV-----SLCLDKKIATQMAKINIIASIL 117
            MD    +  ++    A+ +H++ GIR+L+ D      +L   K+ A     I ++ S+L
Sbjct: 64  IMDSFFVKFIMWGILTALAYHVVVGIRHLLMDFGYLEETLEAGKRSAKISFVITVVLSLL 123

Query: 118 TVLIVW 123
             ++VW
Sbjct: 124 AGVLVW 129


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

 Score = 33.2 bits (75), Expect = 0.017
 Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 2/43 (4%)

Query: 1   MSSIKNNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYLGTPVV 43
           +S+   NRPLSPHL + +   +   SI HRI G    LG  ++
Sbjct: 75  LSAPVANRPLSPHLPLKKPQLSATFSISHRIFG--AALGAAII 115


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

 Score = 32.8 bits (74), Expect = 0.026
 Identities = 17/34 (50%), Positives = 23/34 (67%), Gaps = 2/34 (5%)

Query: 5   KNNRPLSPHLQIYRLIPTMFVSIVHRITGSVVYL 38
           K+ RPLSPHL +Y+      +SI +RI+G  VYL
Sbjct: 122 KSFRPLSPHLSVYQPQMNSMLSIFNRISG--VYL 153


>gnl|CDD|150381 pfam09696, Ctf8, Ctf8.  Ctf8 (chromosome transmissions fidelity
          8) is a component of the Ctf18 RFC-like complex which
          is a DNA clamp loader involved in sister chromatid
          cohesion.
          Length = 107

 Score = 29.5 bits (67), Expect = 0.27
 Identities = 10/24 (41%), Positives = 14/24 (58%)

Query: 21 PTMFVSIVHRITGSVVYLGTPVVV 44
           T++V    R+TG VV L  P+ V
Sbjct: 46 VTLYVGKHQRLTGKVVKLDKPLAV 69


>gnl|CDD|180887 PRK07211, PRK07211, replication factor A; Reviewed.
          Length = 485

 Score = 27.0 bits (60), Expect = 1.6
 Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 6/27 (22%)

Query: 32  TGSVVYLGTPVVVFWFFCIANGEHTLS 58
           TG+VV  G PVV+       +GE T+S
Sbjct: 435 TGTVVQAGDPVVL------DDGEETMS 455


>gnl|CDD|177752 PLN00148, PLN00148, potassium transporter; Provisional.
          Length = 785

 Score = 26.3 bits (58), Expect = 2.1
 Identities = 7/22 (31%), Positives = 11/22 (50%)

Query: 29  HRITGSVVYLGTPVVVFWFFCI 50
           H  T  V ++  P+V+ W   I
Sbjct: 213 HCGTHRVAFMFAPIVIIWLLSI 234


>gnl|CDD|180600 PRK06519, PRK06519, 3-oxoacyl-(acyl carrier protein) synthase II;
           Reviewed.
          Length = 398

 Score = 26.1 bits (58), Expect = 2.6
 Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 11/27 (40%)

Query: 19  LIPTMF-----------VSIVHRITGS 34
           L PT+F           +SIVH++TGS
Sbjct: 141 LRPTLFLAQLSNLLAGNISIVHKVTGS 167


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

 Score = 25.8 bits (56), Expect = 3.0
 Identities = 9/11 (81%), Positives = 10/11 (90%)

Query: 8  RPLSPHLQIYR 18
          RPLSPHL IY+
Sbjct: 5  RPLSPHLPIYK 15


>gnl|CDD|185324 PRK15426, PRK15426, putative diguanylate cyclase YedQ; Provisional.
          Length = 570

 Score = 25.4 bits (56), Expect = 4.1
 Identities = 11/41 (26%), Positives = 14/41 (34%), Gaps = 11/41 (26%)

Query: 54  EHTLSSLRCYMDGSV----------FEVCLFLYTWAVIHHM 84
            HTL        GS+          F   L + +W VI  M
Sbjct: 344 VHTLREGVRGDFGSISIALTLLWALFTAMLLI-SWYVIRRM 383


>gnl|CDD|180293 PRK05857, PRK05857, acyl-CoA synthetase; Validated.
          Length = 540

 Score = 25.4 bits (55), Expect = 4.5
 Identities = 9/25 (36%), Positives = 12/25 (48%)

Query: 49  CIANGEHTLSSLRCYMDGSVFEVCL 73
           C+  GE+T S L      +V   CL
Sbjct: 242 CVTGGENTTSLLEILTTNAVATTCL 266


>gnl|CDD|182474 PRK10456, PRK10456, arginine succinyltransferase; Provisional.
          Length = 344

 Score = 25.5 bits (56), Expect = 4.7
 Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 2/24 (8%)

Query: 11  SPHLQIYRLIPTMFVSIVHRITGS 34
           S  L +Y  +PT+F+S  H  TGS
Sbjct: 98  SKELNVYNALPTLFLSNDH--TGS 119


>gnl|CDD|180502 PRK06273, PRK06273, ferredoxin; Provisional.
          Length = 165

 Score = 25.4 bits (56), Expect = 4.9
 Identities = 10/34 (29%), Positives = 20/34 (58%)

Query: 94  DVSLCLDKKIATQMAKINIIASILTVLIVWIIKD 127
           DVS  L+K +     +++ I+ IL++ +  I+K 
Sbjct: 127 DVSKLLEKPVEISEEQLSKISQILSINLSKIVKK 160


>gnl|CDD|177753 PLN00149, PLN00149, potassium transporter; Provisional.
          Length = 779

 Score = 24.8 bits (54), Expect = 7.4
 Identities = 10/26 (38%), Positives = 15/26 (57%)

Query: 26  SIVHRITGSVVYLGTPVVVFWFFCIA 51
           ++ H  T  V +L  PVV+ W  CI+
Sbjct: 211 ALQHYGTHRVGFLFAPVVLTWLLCIS 236


>gnl|CDD|132287 TIGR03243, arg_catab_AOST, arginine and ornithine
           succinyltransferase subunits.  In many bacteria, the
           sole member of this protein family is arginine
           N-succinyltransferase (EC 2.3.1.109), the AstA protein
           of the arginine succinyltransferase (ast) pathway.
           However, in Pseudomonas aeruginosa and several other
           species, a tandem gene pair encodes alpha and beta
           subunits of a heterodimer that is designated arginine
           and ornithine succinyltransferase (AOST).
          Length = 335

 Score = 24.1 bits (53), Expect = 10.0
 Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 2/24 (8%)

Query: 11  SPHLQIYRLIPTMFVSIVHRITGS 34
           S  L +Y  IPT+   + + +TGS
Sbjct: 96  SRELGVYNKIPTLT--LSNDLTGS 117


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.333    0.144    0.468 

Gapped
Lambda     K      H
   0.267   0.0753    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,077,137
Number of extensions: 117463
Number of successful extensions: 305
Number of sequences better than 10.0: 1
Number of HSP's gapped: 303
Number of HSP's successfully gapped: 32
Length of query: 129
Length of database: 5,994,473
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,201,009
Effective search space: 193246414
Effective search space used: 193246414
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 51 (23.4 bits)