GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS24010 in Pseudomonas fluorescens FW300-N2C3

Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate AO356_18710 AO356_18710 amino acid ABC transporter permease

Query= uniprot:B2TBJ8
         (250 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18710 AO356_18710 amino
           acid ABC transporter permease
          Length = 232

 Score =  190 bits (482), Expect = 2e-53
 Identities = 96/222 (43%), Positives = 143/222 (64%)

Query: 1   MHFDFDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYIL 60
           M FD++ +++ +    + + TTL L   SL  G L +L +  MRVS   + N  A  Y  
Sbjct: 1   MIFDYNVIYEALPLYFSGLLTTLKLLALSLFFGLLAALPLGLMRVSKQPIVNMTAWLYTY 60

Query: 61  VFRGSPLLIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGL 120
           V RG+P+L+Q+FL+YYG+ QF ++RESFLWP L     CA L+ A+ T+ YTAEII G L
Sbjct: 61  VIRGTPMLVQLFLIYYGLAQFAIVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSL 120

Query: 121 MAVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEV 180
            A P G+IEA  ++G+S + L RR++ P ALR+ LP YS E ++++++T+LAS+VT+ ++
Sbjct: 121 RATPNGEIEAAKAMGMSRYKLYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDI 180

Query: 181 TGVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETR 222
           TG A+ +  Q Y   E +I A   YL L F++VRL  + E R
Sbjct: 181 TGAARTVNAQYYLPFEAYITAGAFYLCLTFILVRLFKLAERR 222


Lambda     K      H
   0.331    0.143    0.431 

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: 169
Number of extensions: 5
Number of successful extensions: 1
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: 250
Length of database: 232
Length adjustment: 23
Effective length of query: 227
Effective length of database: 209
Effective search space:    47443
Effective search space used:    47443
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 46 (22.3 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