GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Dehalococcoides mccartyi 195

Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease

Query= uniprot:Q31RN9
         (396 letters)



>NCBI__GCF_000011905.1:WP_010936196.1
          Length = 273

 Score =  125 bits (315), Expect = 1e-33
 Identities = 86/252 (34%), Positives = 139/252 (55%), Gaps = 33/252 (13%)

Query: 157 RFLPTLWGVLFLVGLWLLQGGLGL-RPVSSND-----WSGLLLTLATALISMVCSLPLGI 210
           R  P  W    + G+++L GGL L +P    D     W G+ +T+  A++S    L LG+
Sbjct: 23  RMDPWWW---LVAGVFVLTGGLMLFQPDPFLDIFKYVWVGIGITVLVAVVSYFLMLILGM 79

Query: 211 LLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVMVPLMLDS-----------EWR 259
             ALGR S    +R L+  Y+E+ RG+PL+  L +     P+++ S            ++
Sbjct: 80  FGALGRLSKNTILRGLATFYVEIVRGIPLLVQLIWWYFAFPVIIQSIGQGLNFGPMMNYQ 139

Query: 260 IDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRI 319
            + I+ AI G+T    AY++E  R G+Q+IP+GQ EAA +LG++  Q  R+++LPQALR+
Sbjct: 140 ANPIVMAIWGMTFCYGAYMSEIYRAGIQSIPKGQMEAARSLGMSHTQAMRYVILPQALRV 199

Query: 320 SIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILA---NPAYLGRYAEVYLFLGVLYWL 376
            +P +   F+ LL+DT+L+S V + +++ + R   A   NP       EV+  +G+LY +
Sbjct: 200 VLPPMGNEFIALLKDTSLVSTVAVADMVRLGREFTATNFNP------IEVWTMIGLLYLI 253

Query: 377 CCYGLAQLSRRL 388
               L  LS RL
Sbjct: 254 ----LTLLSSRL 261


Lambda     K      H
   0.329    0.142    0.471 

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: 230
Number of extensions: 12
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: 396
Length of database: 273
Length adjustment: 28
Effective length of query: 368
Effective length of database: 245
Effective search space:    90160
Effective search space used:    90160
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: 49 (23.5 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