GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Marinobacter adhaerens HP15

Align High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate GFF4155 HP15_4095 branched-chain amino acid ABC transporter, ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__Marino:GFF4155
          Length = 271

 Score =  218 bits (555), Expect = 1e-61
 Identities = 106/253 (41%), Positives = 165/253 (65%), Gaps = 2/253 (0%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           ILE+S L++ FGG+ A+  V+ +V E  V ++IGPNGAGKT++FNC++GFY+P  G IR 
Sbjct: 3   ILEISNLSLSFGGVKALQDVSFRVPENTVTTIIGPNGAGKTSLFNCISGFYKPQQGTIRY 62

Query: 65  DGEEIQG-LPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGL-FKTPA 122
            G+ + G +   K A  G+ RTFQN+ LF+ MT ++N+ +  H H+ +  L+ L +  PA
Sbjct: 63  QGQTLPGSIKPPKRAALGLARTFQNIALFRGMTVLDNIKLGAHVHMKSGLLSALAYFGPA 122

Query: 123 FRRSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182
            R       +     ++ + +     +   +L+YG Q+R+E+AR +  +P++LMLDEP A
Sbjct: 123 RREEMAVRKDVEERIIDFLEIDHIRRQPVASLSYGLQKRVELARALAMQPKVLMLDEPVA 182

Query: 183 GLNPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIR 242
           G+N +E +D+   I  +R E  VTVL++EHDM +VM ISDHI V+N G  + +G P  ++
Sbjct: 183 GMNREEKEDMARFILDIREEWGVTVLMVEHDMGMVMDISDHIAVLNFGQVITEGLPADVQ 242

Query: 243 DNPDVIKAYLGEA 255
           +NP+VIKAYLG +
Sbjct: 243 NNPEVIKAYLGNS 255


Lambda     K      H
   0.320    0.137    0.391 

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: 177
Number of extensions: 6
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: 255
Length of database: 271
Length adjustment: 25
Effective length of query: 230
Effective length of database: 246
Effective search space:    56580
Effective search space used:    56580
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: 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