GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araWsh in Rhodobacter viridis JA737

Align Inner-membrane translocator (characterized, see rationale)
to candidate WP_110806514.1 C8J30_RS14100 ABC transporter permease

Query= uniprot:A0KWY6
         (405 letters)



>NCBI__GCF_003217355.1:WP_110806514.1
          Length = 339

 Score =  147 bits (371), Expect = 5e-40
 Identities = 102/309 (33%), Positives = 158/309 (51%), Gaps = 24/309 (7%)

Query: 67  LALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPVALLSIGMSLVIATGGIDLS 126
           +AL   +L  +F   SF       DRL   ++ +    + + ++S+G++ VI  GGIDLS
Sbjct: 31  IALVFEILGWIFQGQSFL---MSIDRLKIMILQV----SVIGIISVGVTQVIIAGGIDLS 83

Query: 127 VGAVMAIAGAVCANLLLVP-----------DISLVTVIAAGLIVGLLAGCINGGLVSFLG 175
            G+V+        +   V            D+  +  IA GL+ G L G ING L+++  
Sbjct: 84  SGSVVGAVAMFAMSFAQVSTYARAVYPDLTDLPAIVPIALGLMAGALVGLINGALIAYAK 143

Query: 176 IQPIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQ 235
           I P +ATL  MV  RG A+   +GQ I+F    FA IG G      MPV I + +     
Sbjct: 144 IPPFIATLGTMVTARGFAKWYTKGQPISFPTDDFAFIGKGM-----MPVAIFLAVAAIFH 198

Query: 236 LLLRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADIQGSDA 295
           + ++ T  G F  A+G N +A+R  GIN +   +  Y +A   AALAGM+  A  Q + A
Sbjct: 199 VAMKYTRYGKFTYAIGANQQAARVSGINVEHHLIKVYVVAATLAALAGMVVAARGQTAQA 258

Query: 296 NNAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIK 355
              GL  ELDA+   VIGG +LTGGR S++ +++G +I   + +      L A +  +IK
Sbjct: 259 -GMGLAYELDAIAMAVIGGVSLTGGRGSILGTMIGMVIFGVIISGFTFLRLDAYYQEMIK 317

Query: 356 AIVILTVLL 364
            ++I+  ++
Sbjct: 318 GVIIVAAVV 326


Lambda     K      H
   0.323    0.136    0.379 

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: 298
Number of extensions: 19
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: 405
Length of database: 339
Length adjustment: 30
Effective length of query: 375
Effective length of database: 309
Effective search space:   115875
Effective search space used:   115875
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 (22.0 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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