GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Azospirillum brasilense Sp245

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS32410 AZOBR_RS32410 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__azobra:AZOBR_RS32410
          Length = 355

 Score =  186 bits (471), Expect = 1e-51
 Identities = 109/334 (32%), Positives = 180/334 (53%), Gaps = 45/334 (13%)

Query: 12  AVALLVLPLILQSFGNAWV-RIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYL 70
           AVA   +P  +   G++++ +IA   +++V+L+  LN V G AGLL +G+ AFY +GAY 
Sbjct: 36  AVAFGAVPAAIVGTGSSYLAQIAITTMIFVILSASLNHVTGTAGLLSIGHAAFYGIGAYA 95

Query: 71  FALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAI 130
            AL+++                 L     + +P A L+AA FG ++  PT++L   Y A+
Sbjct: 96  AALLSTK----------------LGLPFIVTLPAAGLIAALFGFLVALPTMRLVSIYFAV 139

Query: 131 VTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYY 190
            TLG GE+I + L N    V++T GP G+  I  +           E+FG+  +++   Y
Sbjct: 140 ATLGIGEMIYVVLLNW---VDVTRGPMGIRGIPPI-----------ELFGWQADTLLTRY 185

Query: 191 YLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGV 250
               V+ V  V + +RL  S  G A  A+RED+  A +MGIN   +K+ +F +   F G+
Sbjct: 186 LAVAVIAVACVWVLHRLTHSYYGNALRALREDDQCADSMGINVERLKIESFVVATFFAGI 245

Query: 251 SGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGP 310
           +GA+      +++P++F  MES++I+AMVV+GG+G +PG ++GA+ +  LPE LR     
Sbjct: 246 AGALLAHTSAYIAPDNFRFMESILILAMVVVGGLGSLPGAVVGALFMIVLPEALR----- 300

Query: 311 LQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344
                    D    R + +   M + +LL P+G+
Sbjct: 301 ---------DIGDYRMIAVGATMFLSILLLPKGM 325


Lambda     K      H
   0.328    0.144    0.430 

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: 336
Number of extensions: 16
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 355
Length adjustment: 29
Effective length of query: 329
Effective length of database: 326
Effective search space:   107254
Effective search space used:   107254
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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