GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuG in Rhizobium freirei PRF 81

Align Trehalose transport system permease protein SugB (characterized)
to candidate WP_004119214.1 RHSP_RS16125 carbohydrate ABC transporter permease

Query= SwissProt::P9WG01
         (274 letters)



>NCBI__GCF_000359745.1:WP_004119214.1
          Length = 295

 Score =  171 bits (434), Expect = 1e-47
 Identities = 98/268 (36%), Positives = 150/268 (55%), Gaps = 5/268 (1%)

Query: 9   WAVLDTLVVGYALLPVLWIFSLSLKPTSTVKD--GKLIPSTVTFDNYRGIFRGDLFSSAL 66
           W  L  LV    L P ++I   SLK  + V      + P    F+NY   +    F+SA 
Sbjct: 31  WIAL-LLVAAIWLAPFVFIVFTSLKTQADVTSTGAFMPPFDPAFENYSNAWGRGNFASAF 89

Query: 67  INSIGIGLITTVIAVVLGAMAAYAVARLEFPGKRLLIGAALLITMFPSISLVTPLFNIER 126
           +NS  I +I   + ++L AMAAYA+A++     ++++ A +  TM P   ++ PLF +  
Sbjct: 90  LNSAIITVIKVPLGLILSAMAAYALAKIRMRFSKIMLLAIVFGTMIPFQVMLAPLFTLVN 149

Query: 127 AIGLFDTWPGLILPYITFALPLAIYTLSAFFREIPWDLEKAAKMDGATPGQAFRKVIVPL 186
           ++GL DT+PG+ILPYI F +P  ++ L  FF+ IP +L +AA +DGA+    FR++ +P+
Sbjct: 150 SLGLIDTYPGVILPYIAFGVPYQVFILHGFFKGIPKELSEAALIDGASHFTIFRRIFLPV 209

Query: 187 AAPGLVTAAILVFIFAWNDLLLALSLTATKAAITAPVAIANFTGSSQFEEPTGSIAAGAI 246
             P L    IL F+  WN+  +AL L   +   T P+ + +F G  QF    G + A  +
Sbjct: 210 CLPVLAALLILDFVSTWNEFAMALVLLQDQHMWTLPLGLMSFQG--QFSNDYGQLNAAIV 267

Query: 247 VITIPIIVFVLIFQRRIVAGLTSGAVKG 274
           +  +P  +  LIFQR  V+GLTSGAVKG
Sbjct: 268 MTVLPATIVYLIFQRYFVSGLTSGAVKG 295


Lambda     K      H
   0.327    0.141    0.418 

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: 269
Number of extensions: 11
Number of successful extensions: 2
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: 274
Length of database: 295
Length adjustment: 26
Effective length of query: 248
Effective length of database: 269
Effective search space:    66712
Effective search space used:    66712
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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