GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Sphingomonas koreensis DSMZ 15582

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ga0059261_2542 Ga0059261_2542 ABC-type (unclassified) transport system, ATPase component

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__Korea:Ga0059261_2542
          Length = 258

 Score =  115 bits (288), Expect = 9e-31
 Identities = 74/236 (31%), Positives = 124/236 (52%), Gaps = 4/236 (1%)

Query: 12  LQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFE 71
           L V  +   Y     L+ V + V KGE+V L+G NGAGK+T   ++ G  +   G ++ +
Sbjct: 22  LAVVSIAKSYDKRVVLSDVSLSVGKGEVVGLLGPNGAGKTTCFYSVMGLVKPDAGRIMLD 81

Query: 72  GRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLD--NLKHFAEDVEKIFTL 129
           G DIT +P +  A L +   P+   IF  +TV +N+     L   +    A  ++++   
Sbjct: 82  GVDITPLPMYRRAILGLGYLPQETSIFRGLTVAKNISAVLELSEPDKSARAARLDQLLEE 141

Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189
           F   + R A     LSGGE++   I RAL A P ++LLDEP  G+ P+ +  I + +++L
Sbjct: 142 FGLTRLRDAP-AMALSGGERRRAEIARALAADPSIMLLDEPFAGIDPISIADIRDLVKEL 200

Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYLEGG 245
            +   + V + + N    L +  RA ++ +G+V  +GS ++L+A+  VR  YL  G
Sbjct: 201 -KTRNIGVLITDHNVRETLDIVDRASIIYDGRVLFAGSPEDLVADANVRRLYLGEG 255


Lambda     K      H
   0.320    0.137    0.387 

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: 7
Number of successful extensions: 3
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: 247
Length of database: 258
Length adjustment: 24
Effective length of query: 223
Effective length of database: 234
Effective search space:    52182
Effective search space used:    52182
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: 46 (22.3 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