GapMind for catabolism of small carbon sources

 

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

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate Ac3H11_1936 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1936
          Length = 272

 Score =  215 bits (547), Expect = 8e-61
 Identities = 112/234 (47%), Positives = 158/234 (67%), Gaps = 2/234 (0%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           +L    V + YG I+A+  VS++V++GEI  ++G+NGAGK+T+L T+ G      GSI +
Sbjct: 20  LLRLQNVESAYGPIKAIRGVSLQVRRGEIAAVLGSNGAGKTTILKTISGIIDPRKGSIEF 79

Query: 61  EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFF-TDKDDYQVQMDKVLEL 119
           +G+++     + I+R+ +  VPEGR VF  L+V +NL MG +   DKD     ++ V   
Sbjct: 80  QGQDITARDPAAIVRRGLMHVPEGREVFPLLSVRDNLLMGAYTRADKDGVARDIETVFGY 139

Query: 120 FPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQL 179
           FP LKER  Q AG +SGG+QQMLAI RALM+ P+L+LLDEPSLGL+P + ++IFEI+ ++
Sbjct: 140 FPILKERAAQDAGLLSGGQQQMLAISRALMAAPELILLDEPSLGLSPKLTKEIFEIVVRI 199

Query: 180 RRE-GVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232
            RE G T+ LVEQNAN AL  +D  YVLENGRIVM D+   L     +++ YLG
Sbjct: 200 NRERGTTILLVEQNANMALNASDYGYVLENGRIVMEDSCERLREKDDIKEFYLG 253


Lambda     K      H
   0.318    0.136    0.374 

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: 168
Number of extensions: 5
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: 233
Length of database: 272
Length adjustment: 24
Effective length of query: 209
Effective length of database: 248
Effective search space:    51832
Effective search space used:    51832
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: 46 (22.3 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