GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate CA265_RS25230 CA265_RS25230 LPS export ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>FitnessBrowser__Pedo557:CA265_RS25230
          Length = 246

 Score =  151 bits (381), Expect = 1e-41
 Identities = 87/237 (36%), Positives = 138/237 (58%), Gaps = 8/237 (3%)

Query: 3   VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEF 62
           +L+ ENL   Y     V +VSF V++GE+V L+G NGAGKTT    + GL++P+ G+I  
Sbjct: 2   ILRAENLVKKYKQRTVVNNVSFNVSQGEIVGLLGPNGAGKTTSFYMIVGLIKPNEGRIFL 61

Query: 63  LGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMEN----LEMGAFLKKNREENQANLKK 118
             ++I + P  +    G+  + +   VF  LTV +N    LEM      ++EE +  L++
Sbjct: 62  EDEDITEDPMYRRAQKGIGYLAQEASVFRKLTVEDNILAILEMS---NMSKEEQRDKLEE 118

Query: 119 VFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDI 178
           + + F   + RKN+    LSGGE++   + RAL + P  +LLDEP  G+ PI ++EI  I
Sbjct: 119 LINEFSLHKVRKNR-GDLLSGGERRRTEIARALAANPNFILLDEPFAGVDPIAVEEIQSI 177

Query: 179 IQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLG 235
           +  ++ +   +L+ + N  + L+I+DR Y+L  GKI+  G  + LA +E VRK YLG
Sbjct: 178 VAKLKHKNIGILITDHNVQETLSITDRAYLLFEGKILEQGVPEVLAENEMVRKVYLG 234


Lambda     K      H
   0.315    0.134    0.358 

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: 153
Number of extensions: 7
Number of successful extensions: 2
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: 236
Length of database: 246
Length adjustment: 23
Effective length of query: 213
Effective length of database: 223
Effective search space:    47499
Effective search space used:    47499
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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