GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pedobacter sp. GW460-11-11-14-LB5

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 CA265_RS25230 CA265_RS25230 LPS export ABC transporter ATP-binding protein

Query= TCDB::P21629
         (255 letters)



>FitnessBrowser__Pedo557:CA265_RS25230
          Length = 246

 Score =  135 bits (339), Expect = 1e-36
 Identities = 76/249 (30%), Positives = 137/249 (55%), Gaps = 16/249 (6%)

Query: 5   ILEVSGLTMRFGGLLAVNGVNLKVEEKQVVSMIGPNGAGKTTVFNCLTGFYQPTGGLIRL 64
           IL    L  ++     VN V+  V + ++V ++GPNGAGKTT F  + G  +P  G I L
Sbjct: 2   ILRAENLVKKYKQRTVVNNVSFNVSQGEIVGLLGPNGAGKTTSFYMIVGLIKPNEGRIFL 61

Query: 65  DGEEIQGLPGHKIARKGVVRTFQNVRLFKEMTAVENLLVAQHRHLNTNFLAGLFKTPAFR 124
           + E+I   P ++ A+KG+    Q   +F+++T  +N+            LA L  +   +
Sbjct: 62  EDEDITEDPMYRRAQKGIGYLAQEASVFRKLTVEDNI------------LAILEMSNMSK 109

Query: 125 RSEREAMEYAAHWLEEVNLTEFANRSAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184
             +R+ +E     + E +L +        L+ G++RR EIAR +   P  ++LDEP AG+
Sbjct: 110 EEQRDKLE---ELINEFSLHKVRKNRGDLLSGGERRRTEIARALAANPNFILLDEPFAGV 166

Query: 185 NPKETDDLKALIAKLRSEHNVTVLLIEHDMKLVMSISDHIVVINQGAPLADGTPEQIRDN 244
           +P   +++++++AKL+ + N+ +L+ +H+++  +SI+D   ++ +G  L  G PE + +N
Sbjct: 167 DPIAVEEIQSIVAKLKHK-NIGILITDHNVQETLSITDRAYLLFEGKILEQGVPEVLAEN 225

Query: 245 PDVIKAYLG 253
             V K YLG
Sbjct: 226 EMVRKVYLG 234


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: 169
Number of extensions: 9
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: 246
Length adjustment: 24
Effective length of query: 231
Effective length of database: 222
Effective search space:    51282
Effective search space used:    51282
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