GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PfGW456L13_1896 in Burkholderia phytofirmans PsJN

Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate BPHYT_RS05035 BPHYT_RS05035 sugar ABC transporter permease

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896
         (281 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS05035 BPHYT_RS05035 sugar ABC
           transporter permease
          Length = 285

 Score =  369 bits (946), Expect = e-107
 Identities = 185/281 (65%), Positives = 220/281 (78%), Gaps = 9/281 (3%)

Query: 10  ISFSRIAIYATLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAW-- 67
           ++ SR  IYA L L A  +L PL VML TSFK  + +RTGNLL+ PT      WIKAW  
Sbjct: 5   MTISRAVIYAALFLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPPTHWTIDPWIKAWSG 64

Query: 68  -------DVVGGYFWNSVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFL 120
                  D +  +F NSV++ +PAVLIS+ IGA NGYVL+ WRFRG+   F ++L GCF+
Sbjct: 65  ACTGVRCDGMQPFFMNSVRMVIPAVLISSIIGAFNGYVLTHWRFRGADPIFTMILVGCFI 124

Query: 121 PFQTVLLPASFTLGKFGLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDG 180
           PFQ +LLP +   G  GL+NTTTGLV+VHV+YG+AFTT+FFRN+YVSIP  LVKAAR+DG
Sbjct: 125 PFQAILLPMARFEGFLGLSNTTTGLVVVHVIYGIAFTTMFFRNFYVSIPAELVKAARIDG 184

Query: 181 AGFFTIFLKILLPMSIPIVMVCLIWQFTQIWNDFLFGVVFASGDAQPITVALNNLVNTST 240
           AGFFTIF KILLP+S+PI MVCLIWQFTQIWNDFLFG+VF+  D+ PITVALNNLVNTST
Sbjct: 185 AGFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFGIVFSGVDSMPITVALNNLVNTST 244

Query: 241 GAKEYNVDMAAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281
           G KEYNVDMA A+IA LPTLLVYI AG+YF+RGLT+GAVKG
Sbjct: 245 GVKEYNVDMAGAIIAALPTLLVYIIAGRYFVRGLTAGAVKG 285


Lambda     K      H
   0.329    0.143    0.447 

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: 328
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: 281
Length of database: 285
Length adjustment: 26
Effective length of query: 255
Effective length of database: 259
Effective search space:    66045
Effective search space used:    66045
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: 47 (22.7 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