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_083710260.1 BW971_RS17385 ABC transporter ATP-binding protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_900156495.1:WP_083710260.1
          Length = 347

 Score =  136 bits (343), Expect = 5e-37
 Identities = 80/249 (32%), Positives = 134/249 (53%), Gaps = 15/249 (6%)

Query: 2   SVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIE 61
           ++L+V  L+V +G ++A+ DV+F++  GE+  LIG NGAGKTT    ++G+  PS+G + 
Sbjct: 92  ALLEVRGLTVQFGGLKALDDVTFDIKRGEIFGLIGPNGAGKTTCFNAITGVYSPSAGSVT 151

Query: 62  FLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMG-----------AFLKKNR- 109
           F  + + ++   +I   G+++  +   +F  +T +EN+ +G           A L+  R 
Sbjct: 152 FDNKPLGRVKRHEITRRGIARTFQNVRLFGEMTALENVVVGTDARHKTSVFGAALRSRRH 211

Query: 110 ---EENQANLKKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMG 166
              E +  +       F  +  R  + A  L+ G+Q+ L + RAL + PKLL LDEP+ G
Sbjct: 212 YREERDAVDRGMALLEFVGIGARAAEQAKNLAYGDQRRLEIARALATEPKLLCLDEPAAG 271

Query: 167 LAPIFIQEIFDIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASS 226
             P     +  +IQ I+  G TVLLIE +    + +++R  VLE G+ +  GT  E+  +
Sbjct: 272 FNPSEKTALMGLIQKIRDDGYTVLLIEHDMRLVMGVTERIVVLEFGRKIAEGTPSEVREN 331

Query: 227 EEVRKAYLG 235
             V  AYLG
Sbjct: 332 PAVINAYLG 340


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: 181
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: 347
Length adjustment: 26
Effective length of query: 210
Effective length of database: 321
Effective search space:    67410
Effective search space used:    67410
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