GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Dehalococcoides mccartyi 195

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease

Query= TCDB::Q52665
         (434 letters)



>NCBI__GCF_000011905.1:WP_010936196.1
          Length = 273

 Score =  107 bits (267), Expect = 4e-28
 Identities = 76/252 (30%), Positives = 132/252 (52%), Gaps = 30/252 (11%)

Query: 196 FWLYAAAPIEAALQSALPLALPEVDSDQFG----GFLLALVIGVTAIVVSLPLGILLALG 251
           +WL A   +   L   L L  P+   D F     G  + +++ V +  + L LG+  ALG
Sbjct: 28  WWLVAGVFV---LTGGLMLFQPDPFLDIFKYVWVGIGITVLVAVVSYFLMLILGMFGALG 84

Query: 252 RQSDMLIVKSLSVGIIEFVRGVPLITLL----FTASLLLQYFLPPGTNF--------DLI 299
           R S   I++ L+   +E VRG+PL+  L    F   +++Q  +  G NF        + I
Sbjct: 85  RLSKNTILRGLATFYVEIVRGIPLLVQLIWWYFAFPVIIQS-IGQGLNFGPMMNYQANPI 143

Query: 300 LRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPG 359
           +  +  +T    AY++E+ R G+ ++P+GQ EAA +LG+ + QA R +I+PQAL++ +P 
Sbjct: 144 VMAIWGMTFCYGAYMSEIYRAGIQSIPKGQMEAARSLGMSHTQAMRYVILPQALRVVLPP 203

Query: 360 IVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYWEP---YIFVALIFFLFNF 416
           + + FI L KDT+LV+ V        ++++VR    +  T + P   +  + L++ +   
Sbjct: 204 MGNEFIALLKDTSLVSTV-------AVADMVRLGREFTATNFNPIEVWTMIGLLYLILTL 256

Query: 417 SMSRYSMYLERK 428
             SR   Y+E+K
Sbjct: 257 LSSRLINYIEKK 268


Lambda     K      H
   0.329    0.143    0.457 

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: 355
Number of extensions: 20
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: 434
Length of database: 273
Length adjustment: 29
Effective length of query: 405
Effective length of database: 244
Effective search space:    98820
Effective search space used:    98820
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