GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Chryseobacterium arthrosphaerae CC-VM-7

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_083988482.1 BBI00_RS11725 LPS export ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_001684965.1:WP_083988482.1
          Length = 353

 Score =  117 bits (292), Expect = 4e-31
 Identities = 70/224 (31%), Positives = 117/224 (52%), Gaps = 4/224 (1%)

Query: 21  YGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFEGRDITRMPT 80
           YG  + + GV V V +GEIV L+G NGAGK+T    I G  +  +G +  + ++IT    
Sbjct: 12  YGPKKVVKGVSVQVQQGEIVGLLGPNGAGKTTSFYMIVGLVKPTSGKIFLDKQEITTDAM 71

Query: 81  HEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTLFPRLKERHAQ- 139
           +  A+  I    +   +F +++V EN+     L  L    + + K   L      +H + 
Sbjct: 72  YRRAQKGIGYLAQEASVFRKLSVEENIMGVLQLTKLSKREQQI-KCDELIEEFSLQHVRK 130

Query: 140 -RGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLNEAEGLTVF 198
            RG  LSGGE++   I R L   P  +LLDEP  G+ P+ V+ I + +R L + + + + 
Sbjct: 131 NRGDLLSGGERRRTEIARCLATSPNFILLDEPFAGVDPIAVEDIQKIVRSLVD-KNIGIL 189

Query: 199 LVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
           + + N    L ++++ Y+M  GK+   G  ++L  +P+VR AYL
Sbjct: 190 ITDHNVQQTLAITNKTYIMFEGKILKEGLPEDLANDPQVREAYL 233


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: 204
Number of extensions: 10
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: 353
Length adjustment: 26
Effective length of query: 221
Effective length of database: 327
Effective search space:    72267
Effective search space used:    72267
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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