GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Acidovorax sp. GW101-3H11

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Ac3H11_4983 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:G8ALJ0
         (294 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4983
          Length = 280

 Score =  195 bits (495), Expect = 1e-54
 Identities = 112/278 (40%), Positives = 173/278 (62%), Gaps = 20/278 (7%)

Query: 9   TPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRL 68
           TPLL V+ +T+ FGG+ A+  V F    G ITA+IGPNGAGKT+LFN I+GFY P+ G +
Sbjct: 12  TPLLQVQGVTLAFGGVKALTGVGFDVLPGSITAVIGPNGAGKTSLFNTISGFYRPSQGSI 71

Query: 69  TLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFS 128
             +  D     + R+P  + + +  + R+FQNI LF GM+VL+N+ + +H  L       
Sbjct: 72  RFQGQD-----ITRVPAPQRA-RLGLGRSFQNIALFRGMTVLDNIKLGRHAHL------K 119

Query: 129 IAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWE------AGNLPYGAQRRLEIARA 182
              L  L  + R  RE  +L +   +R+  ++F + +         LPYG Q+R+E+ARA
Sbjct: 120 TNVLDALLYFGRARREEAELRRDIEERI--IDFLEIDHIRHAPVSALPYGLQKRVEMARA 177

Query: 183 MCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVL 242
           +  +P +L LDEP AG+N  E+ ++A  +  +R+E  + VL++EHDM +VM +SDHVVVL
Sbjct: 178 LAMQPQILMLDEPVAGMNREETEDMARFILDVREEWGVTVLMVEHDMGMVMDLSDHVVVL 237

Query: 243 DYGRKISDGDPAFVKNDPAVIRAYLGEEEDEELPPEIK 280
           ++G+ I+ G PA V+ +P VIRAYLG  +  +L  +++
Sbjct: 238 NFGQVIAQGTPAAVQANPEVIRAYLGAGDVGDLRAKLQ 275


Lambda     K      H
   0.319    0.137    0.397 

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: 182
Number of extensions: 6
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: 294
Length of database: 280
Length adjustment: 26
Effective length of query: 268
Effective length of database: 254
Effective search space:    68072
Effective search space used:    68072
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: 47 (22.7 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