GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Burkholderia phytofirmans PsJN

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate BPHYT_RS16105 BPHYT_RS16105 mannitol ABC transporter permease

Query= reanno::psRCH2:GFF851
         (296 letters)



>FitnessBrowser__BFirm:BPHYT_RS16105
          Length = 291

 Score =  105 bits (262), Expect = 1e-27
 Identities = 75/210 (35%), Positives = 105/210 (50%), Gaps = 6/210 (2%)

Query: 86  WNSVKIAFVSSILILLLSTTSAYAFARMRFGGKAPILKSMLIFQMFPPVLSLVAIYALFD 145
           WNS+ I+   +IL L+L+  +AYA A         +L  ML  +M P V  LV IY L+ 
Sbjct: 88  WNSILISAGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLLWK 147

Query: 146 QLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYFESIDASLEEAAIVDGATTWQAFFH 205
             G     L  +  G VIV +L  + + +W    YF  I   + EA  +DGA TWQ   +
Sbjct: 148 NSG-----LLDSVSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVY 202

Query: 206 ILLPMSVPILAVVFILAFITSVTEYPIASVLLMDVDKLTLSVGAQQYLYPQNYLWGDFAA 265
           +L+PMS+P LA   +L  I S  E    S+ L   +   L+V    Y  P+   W   +A
Sbjct: 203 LLMPMSLPGLASTALLLVILSWNE-AFWSINLSSSNAAPLTVFIASYSSPEGLFWAKLSA 261

Query: 266 AAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295
           A++L+  PI  V    QK +V GLT G VK
Sbjct: 262 ASLLAVAPILIVGWLSQKQLVRGLTFGAVK 291


Lambda     K      H
   0.327    0.139    0.433 

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: 249
Number of extensions: 21
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: 296
Length of database: 291
Length adjustment: 26
Effective length of query: 270
Effective length of database: 265
Effective search space:    71550
Effective search space used:    71550
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: 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:

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