GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04257 in Ruegeria conchae TW15

Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate WP_010438517.1 G7G_RS0103680 carbohydrate ABC transporter permease

Query= reanno::Smeli:SMc04257
         (305 letters)



>NCBI__GCF_000192475.1:WP_010438517.1
          Length = 299

 Score =  320 bits (819), Expect = 3e-92
 Identities = 151/275 (54%), Positives = 203/275 (73%)

Query: 31  IVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPWVKAWAEACTGLN 90
           ++Y  L + ALYYL+PL+VM+ TSLK + EIR G++ + P E++F+ W  AW+ ACTG+ 
Sbjct: 25  LLYVLLGLFALYYLMPLFVMLTTSLKSLEEIRTGSLISLPREVSFDAWKTAWSGACTGIQ 84

Query: 91  CDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILIVGAFIPYQVMI 150
           C+GL   FWNSV I VP+V IS  + ++NGY +A WRFKGA++ F++++ G FIP+QV++
Sbjct: 85  CEGLRPYFWNSVLIAVPAVAISTLLGALNGYVVAQWRFKGANIIFSLMLFGCFIPFQVVL 144

Query: 151 YPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFKAARVDGAGFWTI 210
            P+  +L  MG+ GT+ GLI VH I+G+   TL FRNY+  +P EL KAARVDGAGF  I
Sbjct: 145 LPMARLLGIMGIAGTIPGLIFVHVIYGLGFTTLFFRNYYVTIPAELTKAARVDGAGFMRI 204

Query: 211 YFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNNIVNSVQGVKEYN 270
           ++ I LP+SLPI VV +I Q T IWNDFLFGV F++    P+TV LNNIVNS  GVKEYN
Sbjct: 205 FWSIFLPLSLPIIVVTVIWQFTQIWNDFLFGVSFSQAGTQPVTVALNNIVNSTTGVKEYN 264

Query: 271 VNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305
           V+MAA I+ GL  L VY V+G+ F+RG+ AG+VKG
Sbjct: 265 VDMAAAIIAGLPTLLVYVVAGKYFIRGLTAGSVKG 299


Lambda     K      H
   0.329    0.145    0.450 

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: 303
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: 305
Length of database: 299
Length adjustment: 27
Effective length of query: 278
Effective length of database: 272
Effective search space:    75616
Effective search space used:    75616
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 (21.8 bits)
S2: 48 (23.1 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