GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Williamsia sterculiae CPCC 203464

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_076477131.1 BW971_RS05160 ATP-binding cassette domain-containing protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_900156495.1:WP_076477131.1
          Length = 338

 Score =  115 bits (287), Expect = 1e-30
 Identities = 72/221 (32%), Positives = 122/221 (55%), Gaps = 4/221 (1%)

Query: 4   LKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFL 63
           ++V  L+  +G  +AV  + F+V  G V  L+G NGAGKTT +R +S L+RP +G+I  L
Sbjct: 12  VEVRGLTKSFGSHRAVDGIDFDVPRGIVCGLLGPNGAGKTTTVRMMSTLLRPDAGRISVL 71

Query: 64  GQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEM-GAFLKKNREENQANLKKVFSR 122
           G ++  +     V   +S   +   V   LT  ENLE+ G  L +   + +   + +  +
Sbjct: 72  GHDV--VSDSTAVRSLISLTGQSASVDNDLTAAENLEIYGRLLGQRGSQARRRARDLIDQ 129

Query: 123 FPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDI 182
           F  L    N+     SGG ++ L +  +++  P LL LDEP+ GL P    +++DI++ +
Sbjct: 130 FG-LSAAGNRPLRHYSGGMRRRLDLAASMIRRPALLFLDEPTTGLDPRTRAQLWDIVRSV 188

Query: 183 QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKEL 223
              GTTV+L  Q  ++A A++D+  V++ G++V  GT + L
Sbjct: 189 VAAGTTVVLTTQYLDEADALADQLVVIDNGRVVGQGTPESL 229


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: 165
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: 338
Length adjustment: 26
Effective length of query: 210
Effective length of database: 312
Effective search space:    65520
Effective search space used:    65520
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: 47 (22.7 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