GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artM in Burkholderia phytofirmans PsJN

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate BPHYT_RS21915 BPHYT_RS21915 ABC transporter permease

Query= TCDB::Q9HU29
         (230 letters)



>FitnessBrowser__BFirm:BPHYT_RS21915
          Length = 222

 Score =  142 bits (358), Expect = 5e-39
 Identities = 83/218 (38%), Positives = 131/218 (60%), Gaps = 10/218 (4%)

Query: 7   ILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARAS-RHWYVRAVPYAYIFFFRGTP 65
           ++  +P +L GA +T+E+ A ++     L L +GI R + +   V     AY+ FFRGTP
Sbjct: 8   VIAGLPDILHGAVVTVEVTAASLALSCVLGLLIGIGRLTPKRRIVYGFCTAYLTFFRGTP 67

Query: 66  LLLQLFIVYYGLAQFEEVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPVG 125
           LL+QLF++++GL QF           L   + C +L + L++AAY++EI+RGAI SV  G
Sbjct: 68  LLVQLFLLFFGLPQFG---------ILLPAFVCGMLGLGLYSAAYVSEIVRGAIQSVDRG 118

Query: 126 EVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMART 185
           ++EAAR++GMS  QA+  IILP+A+   +P   NE I ++K SA+V  +T+ D+M   + 
Sbjct: 119 QMEAARSIGMSSGQAMRAIILPQAIVRMIPPLGNEFIALIKNSALVSLLTIDDLMHEGQK 178

Query: 186 IIARTYESMLFFCLAGALYLVITIVLTRIFRLIERWLR 223
           II+ +Y S+  +     +YLV+T         +ER LR
Sbjct: 179 IISVSYRSLEVYLAIALVYLVLTQATNYALHRVERHLR 216


Lambda     K      H
   0.332    0.142    0.443 

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: 127
Number of extensions: 4
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: 230
Length of database: 222
Length adjustment: 22
Effective length of query: 208
Effective length of database: 200
Effective search space:    41600
Effective search space used:    41600
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 (22.0 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:

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