GapMind for catabolism of small carbon sources

 

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

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component

Query= TCDB::Q9R9Q4
         (342 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2941
          Length = 350

 Score =  342 bits (878), Expect = 6e-99
 Identities = 191/346 (55%), Positives = 237/346 (68%), Gaps = 14/346 (4%)

Query: 1   MAELQLRDIRKSFGAFDVIKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTL 60
           MA LQLR I K FG    IKG+ + I+ GEF+VFVGPSGCGKSTLLRLIAGLE I  G+L
Sbjct: 1   MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60

Query: 61  AFDGQIVNQLTPSRRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEM 120
             DG+ +     S+R +AMVFQSYALYPHM+VYENM+F ++LA  DKQ   ++V+ AA +
Sbjct: 61  MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120

Query: 121 LQLTPYLERLPRQLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLH 180
           L LT YL+R P++LSGGQRQRVAIGRAIVR PKVFLFDEPLSNLDAALR  TR+EIAKLH
Sbjct: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180

Query: 181 RSMHKTTMIYVTHDQVEAMTLADRICVLRDGLVEQIGTPLELYETPNSVFVAGFIGSPKM 240
           R +  TT IYVTHDQVEAMTLADR+ VLRDG++EQ+GTPLELY+ P + FVA FIG+P+M
Sbjct: 181 RDLGATT-IYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQM 239

Query: 241 NFL----------SGAFAEPYKA--DTIGIRAEHLEIDEQGG-EWSGTVIHSEMLGSDSY 287
           N +            A A P  A    IG+R E++ +   G     G V   E LG+++ 
Sbjct: 240 NVVPVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQVDLIEALGAETL 299

Query: 288 IYLDIGTGEPVIVRESGIAKHQPGQTIRISPAAGQVHRFDAGGRAL 333
           IY+    G   + R++     + G  + +   A Q H FD  GR +
Sbjct: 300 IYVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFDTAGRVV 345


Lambda     K      H
   0.321    0.138    0.396 

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: 390
Number of extensions: 17
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: 342
Length of database: 350
Length adjustment: 29
Effective length of query: 313
Effective length of database: 321
Effective search space:   100473
Effective search space used:   100473
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 (21.9 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