GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Cronobacter condimenti 1330

Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate WP_007665545.1 BN137_RS16135 carbohydrate ABC transporter permease

Query= reanno::BFirm:BPHYT_RS16105
         (291 letters)



>NCBI__GCF_000319285.1:WP_007665545.1
          Length = 281

 Score =  137 bits (345), Expect = 3e-37
 Identities = 83/263 (31%), Positives = 137/263 (52%), Gaps = 8/263 (3%)

Query: 35  AWLVALLLFFPIFWMTITAFKTEQQAYASSLFFIPT---LDSFREVFARSNYFSFAWNSI 91
           A +  L   FP ++  I++ +  Q+ +  + F  PT    D++      +       NS+
Sbjct: 20  ALMACLFCVFPFYYAIISSLREGQELFTPAYF--PTGWHWDNYVVALVDNGIARSLLNSV 77

Query: 92  LISAGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLLWKNSGL 151
           L++A    LCL ++V AA+A+A  P R  + +L  +L   M P V VL  ++ L +  GL
Sbjct: 78  LVAAVTVGLCLFVSVTAAFALARVPFRGRRVLLFTILCVSMFPQVAVLTGMFELVRFLGL 137

Query: 152 LDSVSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVYLLMPMSLPG 211
            DS+  LVI YT  +LP  VW+  T+   IP ++ EA  +DGA T   I  +  P+  P 
Sbjct: 138 YDSLGALVISYTTFSLPFTVWVLTTFMKSIPVELEEAAIVDGAKTGTIIRRIFAPVLAPA 197

Query: 212 LASTALLLVILSWNEAFWSINL---SSSNAAPLTVFIASYSSPEGLFWAKLSAASLLAVA 268
           + +T LL  I +WNE  +++           P+ + + S +S   L W  + AAS++   
Sbjct: 198 MVTTGLLAFIGAWNEFMFALTFIISGDKRTVPVAISLFSGASSYELPWGSIMAASVVVTL 257

Query: 269 PILIVGWLSQKQLVRGLTFGAVK 291
           PI+++  + QK++V GLT GA+K
Sbjct: 258 PIIVLVLIFQKRIVSGLTSGAIK 280


Lambda     K      H
   0.326    0.136    0.421 

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: 232
Number of extensions: 12
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: 291
Length of database: 281
Length adjustment: 26
Effective length of query: 265
Effective length of database: 255
Effective search space:    67575
Effective search space used:    67575
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