GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5404 in Dehalococcoides mccartyi 195

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>NCBI__GCF_000011905.1:WP_010936196.1
          Length = 273

 Score =  115 bits (287), Expect = 2e-30
 Identities = 71/215 (33%), Positives = 118/215 (54%), Gaps = 14/215 (6%)

Query: 155 WGGLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSS 214
           W G+ +T+++A V     L LG+  ALGR S    +R +   ++E  RG+PL+  L    
Sbjct: 57  WVGIGITVLVAVVSYFLMLILGMFGALGRLSKNTILRGLATFYVEIVRGIPLLVQLIWWY 116

Query: 215 VMLPLFLP---EGMNFDKLLR--------ALIGVILFQSAYIAEVVRGGLQAIPKGQYEA 263
              P+ +    +G+NF  ++         A+ G+     AY++E+ R G+Q+IPKGQ EA
Sbjct: 117 FAFPVIIQSIGQGLNFGPMMNYQANPIVMAIWGMTFCYGAYMSEIYRAGIQSIPKGQMEA 176

Query: 264 AAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAAAD 323
           A ++G+ + ++M  VILPQAL++V+P + N FIAL KDTSLV  + + D++   ++  A 
Sbjct: 177 ARSLGMSHTQAMRYVILPQALRVVLPPMGNEFIALLKDTSLVSTVAVADMVRLGREFTAT 236

Query: 324 PKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERK 358
                   E +    L++ I     SR   ++E+K
Sbjct: 237 N---FNPIEVWTMIGLLYLILTLLSSRLINYIEKK 268


Lambda     K      H
   0.330    0.144    0.469 

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: 337
Number of extensions: 23
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: 365
Length of database: 273
Length adjustment: 27
Effective length of query: 338
Effective length of database: 246
Effective search space:    83148
Effective search space used:    83148
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 (21.9 bits)
S2: 48 (23.1 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