GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artJ in Methanospirillum lacunae Ki8-1

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding 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 WP_109969946.1 DK846_RS15725 basic amino acid ABC transporter substrate-binding protein

Query= TCDB::Q9HU31
         (250 letters)



>NCBI__GCF_003173355.1:WP_109969946.1
          Length = 270

 Score =  133 bits (335), Expect = 3e-36
 Identities = 83/223 (37%), Positives = 114/223 (51%), Gaps = 10/223 (4%)

Query: 28  RIGTEGAYPPFNGIDASGQAVGFDLDIGKALCAKMKTECEVVTSDWDGIIPALNAKKFDF 87
           R+G +  YPPF  +   G+  GFD++  K +      E E     WDGIIPALNA K D 
Sbjct: 49  RVGIDPVYPPFTMMSEKGEPTGFDVESLKWIAKDQGFEAEFQGIAWDGIIPALNANKIDM 108

Query: 88  IVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFKTDKDSLKGKVIGAQRATIAGTWL 147
           + A M+ITDERK+ VDF+ PY+T     V  +      D+       IG QR   A  W+
Sbjct: 109 VYAGMTITDERKEKVDFSKPYWTVNQTVVTKQGSPITMDQVKSGKATIGTQRGCTAAIWV 168

Query: 148 EDNMAD-----VVTIKLYDTQENAYLDLSSGRLDGVLADKFVQYDWLKSDAGKEFEFKGE 202
           EDN+ +        +K YD    A  DL +GR D V+ D  V  D ++   GK  +  G 
Sbjct: 169 EDNLVNKSLMSADNLKQYDNTPLAVEDLVAGRTDAVIYDSTVINDIIE---GKPVQKIGS 225

Query: 203 PVFDNDKIGIAVRKGD-PLREKLNAALKEIVADGTYKKINDKY 244
            +  N++ GIAVRK D  L +KLN  L  ++A   +K +  KY
Sbjct: 226 -IETNEQFGIAVRKSDAELLKKLNTGLDHLMASPDWKALVQKY 267


Lambda     K      H
   0.317    0.135    0.392 

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: 181
Number of extensions: 11
Number of successful extensions: 5
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: 270
Length adjustment: 24
Effective length of query: 226
Effective length of database: 246
Effective search space:    55596
Effective search space used:    55596
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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