GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artQ in Dehalococcoides mccartyi 195

Align ABC transporter for L-Arginine, permease component 2 (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease

Query= reanno::BFirm:BPHYT_RS07675
         (229 letters)



>NCBI__GCF_000011905.1:WP_010936196.1
          Length = 273

 Score =  127 bits (320), Expect = 2e-34
 Identities = 63/206 (30%), Positives = 120/206 (58%), Gaps = 3/206 (1%)

Query: 17  TIELSVLSLAAAVLLGLAGAAAKLSFNRPLRAIATGYTTLIRSVPDLVLMLLLFYSIQIA 76
           T+ ++V+S    ++LG+ GA  +LS N  LR +AT Y  ++R +P LV ++  +++  + 
Sbjct: 63  TVLVAVVSYFLMLILGMFGALGRLSKNTILRGLATFYVEIVRGIPLLVQLIWWYFAFPVI 122

Query: 77  VNNLTDALN---LPQFDIDPFVAGVLTLGFIYGAYFTETFRGAFLAVPRGQLEAGSAYGM 133
           + ++   LN   +  +  +P V  +  + F YGAY +E +R    ++P+GQ+EA  + GM
Sbjct: 123 IQSIGQGLNFGPMMNYQANPIVMAIWGMTFCYGAYMSEIYRAGIQSIPKGQMEAARSLGM 182

Query: 134 SGARVFTRILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADVVKAAQDAGKSTFNMFF 193
           S  +    ++ PQ +R  LP +GN +  L+K T+LVS + +AD+V+  ++   + FN   
Sbjct: 183 SHTQAMRYVILPQALRVVLPPMGNEFIALLKDTSLVSTVAVADMVRLGREFTATNFNPIE 242

Query: 194 FILVAALIYLAITTASNLVLIWLEKR 219
              +  L+YL +T  S+ ++ ++EK+
Sbjct: 243 VWTMIGLLYLILTLLSSRLINYIEKK 268


Lambda     K      H
   0.329    0.142    0.411 

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: 155
Number of extensions: 6
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: 229
Length of database: 273
Length adjustment: 24
Effective length of query: 205
Effective length of database: 249
Effective search space:    51045
Effective search space used:    51045
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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