GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artM in Pseudomonas stutzeri RCH2

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 GFF18 Psest_0018 ectoine/hydroxyectoine ABC transporter, permease protein EhuC

Query= TCDB::Q9HU29
         (230 letters)



>FitnessBrowser__psRCH2:GFF18
          Length = 219

 Score =  101 bits (251), Expect = 1e-26
 Identities = 74/217 (34%), Positives = 119/217 (54%), Gaps = 9/217 (4%)

Query: 7   ILKWMPKMLQGAALTLELLAIAVVAGLALALPLGIARASRHWYVRAVPYAYIFFFRGTPL 66
           +++ +P +LQGA +T+++     +  +A AL   +AR S    +R +   YI  FRG+ L
Sbjct: 1   MIELLPLLLQGAWVTVKVTFFGSLLAIACALIAALARLSPVAPLRWLAITYIEVFRGSSL 60

Query: 67  LLQLFIVYYGLAQFE-EVRKSAFWPYLRDPYWCALLTMTLHTAAYIAEILRGAIHSVPVG 125
           L+QLF +Y+ L      +  SAF          A++ + L+  AY AE+LRGAI SV  G
Sbjct: 61  LVQLFWLYFVLPMPPFNIEMSAFA--------VAVVGLGLNIGAYGAEVLRGAIRSVHRG 112

Query: 126 EVEAARALGMSRRQALWHIILPRAVRIGLPAYSNEVILMLKASAVVYTVTLFDIMGMART 185
           + EA +AL M+    +  IILP+A+   +P  +N +I +LK +++V  +TL D+   AR 
Sbjct: 113 QHEACQALNMTPLTRMRRIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDLAFRARQ 172

Query: 186 IIARTYESMLFFCLAGALYLVITIVLTRIFRLIERWL 222
           +   T  +M  F LA  +Y V+   +    R +ER L
Sbjct: 173 LDQATLMTMEIFGLALVIYFVLAQTINFGMRQLERRL 209


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: 138
Number of extensions: 8
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: 219
Length adjustment: 22
Effective length of query: 208
Effective length of database: 197
Effective search space:    40976
Effective search space used:    40976
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