GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapM in Dehalococcoides mccartyi 195

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease

Query= reanno::Smeli:SMc02120
         (384 letters)



>NCBI__GCF_000011905.1:WP_010936196.1
          Length = 273

 Score =  129 bits (323), Expect = 1e-34
 Identities = 74/217 (34%), Positives = 125/217 (57%), Gaps = 16/217 (7%)

Query: 172 LWGGLMVTLVLSFVGIAVSLPLGILLALGRRSNMPVIKMLCTVFIEVIRGVPLITVLFMA 231
           +W G+ +T++++ V   + L LG+  ALGR S   +++ L T ++E++RG+PL+  L   
Sbjct: 56  VWVGIGITVLVAVVSYFLMLILGMFGALGRLSKNTILRGLATFYVEIVRGIPLLVQLIWW 115

Query: 232 SVMLPLFLP---QGVTFDKFLR--------ALIGVSLFASAYMAEVVRGGLQAIPKGQYE 280
               P+ +    QG+ F   +         A+ G++    AYM+E+ R G+Q+IPKGQ E
Sbjct: 116 YFAFPVIIQSIGQGLNFGPMMNYQANPIVMAIWGMTFCYGAYMSEIYRAGIQSIPKGQME 175

Query: 281 GADSLGLSFWQKMGFIVLPQALKLVIPGIVNTFIGLFKDTSLVSIIGMFDLLGIVRLNFS 340
            A SLG+S  Q M +++LPQAL++V+P + N FI L KDTSLVS + + D++ + R  F+
Sbjct: 176 AARSLGMSHTQAMRYVILPQALRVVLPPMGNEFIALLKDTSLVSTVAVADMVRLGR-EFT 234

Query: 341 DTNWATAVTPLTGLIFAGFVFWLFCFGMSRYSGFMER 377
            TN+     P+      G ++ +     SR   ++E+
Sbjct: 235 ATNF----NPIEVWTMIGLLYLILTLLSSRLINYIEK 267


Lambda     K      H
   0.329    0.144    0.454 

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: 284
Number of extensions: 16
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: 384
Length of database: 273
Length adjustment: 28
Effective length of query: 356
Effective length of database: 245
Effective search space:    87220
Effective search space used:    87220
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: 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