GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Acidovorax sp. GW101-3H11

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_1937 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1937
          Length = 279

 Score =  201 bits (512), Expect = 1e-56
 Identities = 107/267 (40%), Positives = 164/267 (61%), Gaps = 4/267 (1%)

Query: 9   MSDDTLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTM 68
           M++DTLL  ++LS++FGG++A+N+ SF+ +RG++  LIGPNGAGKTTVFN I+  Y PT 
Sbjct: 1   MTNDTLLSAQNLSVRFGGVLAVNNVSFDVRRGEVFTLIGPNGAGKTTVFNLISRIYTPTT 60

Query: 69  GMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKAS 128
           G I +    G    L   P  ++     +ARTFQNI LF   +VL NLL+ +H +   + 
Sbjct: 61  GTIAYAGPGGAMLPLTDQPPHKVASLG-IARTFQNIELFEHASVLHNLLIGRHTQQHSSL 119

Query: 129 GYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCT 188
              +     V   + +A E  E     ++  DL    D     LPYG ++ +E+ARA+CT
Sbjct: 120 WAEMFFTRKVREGEIQAREKAEQI---IDFLDLQHYRDTMVAGLPYGVRKVVELARALCT 176

Query: 189 GPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYG 248
            P+LL LDEP++GLN  E+  +   ++ I+ E G ++L++EHDMS+V ++SD V+ +  G
Sbjct: 177 EPKLLLLDEPSSGLNVEETDDMAFWIQDIQHELGITVLMVEHDMSLVSKVSDRVLAMNQG 236

Query: 249 QKISDGTPDHVKNDPRVIAAYLGVEDE 275
           + ++ GTP  V+  P V+ AYLG  D+
Sbjct: 237 EVVAMGTPREVQTHPGVVEAYLGTIDD 263


Lambda     K      H
   0.318    0.136    0.386 

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: 209
Number of extensions: 11
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: 292
Length of database: 279
Length adjustment: 26
Effective length of query: 266
Effective length of database: 253
Effective search space:    67298
Effective search space used:    67298
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: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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