GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ecfA2 in Sphingomonas koreensis DSMZ 15582

Align Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale)
to candidate Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)

Query= uniprot:P70970
         (276 letters)



>FitnessBrowser__Korea:Ga0059261_3653
          Length = 276

 Score =  121 bits (303), Expect = 2e-32
 Identities = 78/226 (34%), Positives = 126/226 (55%), Gaps = 16/226 (7%)

Query: 6   ERLALYDINASIKEGSYVAVIGHTGSGKSTLLQHLNGLLKPT-----KGQISLGSTVIQA 60
           E+ A+ D++  +   +  A IG +G GKST L+ LN +         +G+I+L    I  
Sbjct: 40  EKQAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVEGEITLDGENIY- 98

Query: 61  GKKNKDLKKLRKKVGIVFQFPEHQLFEETVLKDISFGPMNFGVK--KEDAEQKAREMLQL 118
             K+ D+ +LR +VG+VFQ P    F +++ +++++GP   G+   K D +Q     L+ 
Sbjct: 99  -DKSMDVVQLRARVGMVFQKPNP--FPKSIYENVAYGPRIHGLARAKGDMDQIVERSLKR 155

Query: 119 VGLSEELLDR---SPFELSGGQMRRVAIAGVLAMDPEVLVLDEPTAGLDPRGRKEIMDMF 175
            GL EE+ DR   S   LSGGQ +R+ IA  +A+DPEV+++DEP + LDP    +I ++ 
Sbjct: 156 AGLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIATAKIEELI 215

Query: 176 YELHQRGNLTTILVTHSMEDAAAYADEMIVMHKGTIQASGSPRDLF 221
           +EL  RG    ++VTH+M+ AA  +      H GT+   G    +F
Sbjct: 216 HEL--RGRYAIVIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQIF 259


Lambda     K      H
   0.318    0.136    0.380 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 146
Number of extensions: 6
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 276
Length of database: 276
Length adjustment: 25
Effective length of query: 251
Effective length of database: 251
Effective search space:    63001
Effective search space used:    63001
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory