GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_12060 in Sinorhizobium meliloti 1021

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate SM_b21375 SM_b21375 sugar uptake ABC transporter permease

Query= uniprot:A0A1N7UKA9
         (325 letters)



>lcl|FitnessBrowser__Smeli:SM_b21375 SM_b21375 sugar uptake ABC
           transporter permease
          Length = 320

 Score =  254 bits (648), Expect = 3e-72
 Identities = 139/317 (43%), Positives = 208/317 (65%), Gaps = 4/317 (1%)

Query: 11  TAAPRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTY 70
           TAA    +R      G+ L  ++LC+V +F +  FMT  N+M+IL+Q ++  I A GMT+
Sbjct: 5   TAAKAALVRALKQYGGIFLSLVMLCIVFSFFNPRFMTVVNFMNILQQVAVVAIAAFGMTW 64

Query: 71  VILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIP 130
           VIL   IDLSVGSI+A AG+  A     G G   A++  + AGA++G++NG + A L +P
Sbjct: 65  VILLGEIDLSVGSIIAVAGMVGAQCFAFGMGFAPAIALTLAAGALMGMLNGVLTAKLLLP 124

Query: 131 PFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPIIIFAVVAL--IFW 188
            F+ T+  + I RGM  +  +G+P     + + A+G      +G+PIII+ V  L  I  
Sbjct: 125 SFIVTVATMGIYRGMVSLPTNGAPAMIENETWTAIGTESF--LGLPIIIWVVAVLFVINQ 182

Query: 189 MVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALP 248
           +VL  T++GR  Y  GGN ++A  SGI V ++   ++++SG++A ++GV+LS+R  SA  
Sbjct: 183 IVLSKTSFGRRAYLTGGNREAAVYSGIKVDRLKILIFMISGVMAAISGVLLSSRLFSAQT 242

Query: 249 QAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKG 308
            AG+SYELDAIAA V+GGTSL+GG G++VGTL GAL+IGV+NNG+N+L V  +YQ + KG
Sbjct: 243 NAGMSYELDAIAAAVLGGTSLAGGVGTMVGTLIGALIIGVMNNGMNMLSVPYFYQLIVKG 302

Query: 309 LIIVFAVLIDVWRKKKR 325
           L+I+ AV +DV  K+ +
Sbjct: 303 LVILVAVWLDVRAKQAK 319


Lambda     K      H
   0.326    0.141    0.412 

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: 290
Number of extensions: 20
Number of successful extensions: 1
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: 325
Length of database: 320
Length adjustment: 28
Effective length of query: 297
Effective length of database: 292
Effective search space:    86724
Effective search space used:    86724
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 (21.6 bits)
S2: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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