GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Dethiosulfovibrio salsuginis USBA 82

Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate WP_085545458.1 B9Y55_RS11270 dicarboxylate/amino acid:cation symporter

Query= TCDB::Q01857
         (444 letters)



>NCBI__GCF_900177735.1:WP_085545458.1
          Length = 400

 Score =  238 bits (606), Expect = 3e-67
 Identities = 141/411 (34%), Positives = 231/411 (56%), Gaps = 15/411 (3%)

Query: 9   VAGSKGKKPFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFL 68
           ++ SK   P    + +  ++ IAAG  LG   P++   ++P+G  FI L+KM+I P++F 
Sbjct: 1   MSNSKKGVPLIWRITIGFVLGIAAGAFLG---PKVSI-VEPVGKVFITLLKMLIVPLVFS 56

Query: 69  TVATGIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPA 128
           ++  G++ + + + +GR+  K +L +L  + +A++IGL + +  QPG+GM I+       
Sbjct: 57  SLVVGVSSIGEPKTLGRIGVKTILIYLMTTAVAIVIGLGMGHFFQPGSGMAIEGVE---- 112

Query: 129 AVATFAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVV 188
           A A  AA A  + I+G    + P   V A A G +LQ++ F++ FGIA  + G+KG+ V+
Sbjct: 113 AAAGRAAPALSEVIIG----MFPDNPVQALAQGHMLQIIVFALFFGIAAMLAGDKGKPVI 168

Query: 189 NFLNSLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVF 248
           +F+ S+   ++K+  ++M  AP G F  +A T+ KYG+  +A  A +IG  Y+  ++   
Sbjct: 169 SFMESMAETMYKVTDLVMNLAPYGVFALIAVTVSKYGLSVLAPFAKVIGAVYLGCIVHAI 228

Query: 249 IVL-GAVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMN-KMEKAGCKRSVVGLV 306
           +V  G VA     S +   + I+E  L    T SS A LP  M    E  G    +   V
Sbjct: 229 VVYSGLVAVVTKKSPIWFFKGIQEASLTAFVTRSSSATLPVTMTCTQENMGISEKISSFV 288

Query: 307 IPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFIT 366
           +P G + N+DGT +Y  + ALFIAQA GI LS G Q+ +++ A L+S G AG+ GAG I 
Sbjct: 289 LPLGATINMDGTALYQGVCALFIAQAFGIDLSIGAQVGIIVTATLASVGTAGVPGAGLIM 348

Query: 367 LAATLSVVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENE 417
           L   ++    +P+ G+A++ GID  +   R   N+ G+A  T V+A+ E E
Sbjct: 349 LTLVVTQA-GLPMEGVAMVAGIDAVLDMARTSLNVTGDACVTAVIAKTEGE 398


Lambda     K      H
   0.324    0.139    0.393 

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: 437
Number of extensions: 28
Number of successful extensions: 5
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: 444
Length of database: 400
Length adjustment: 32
Effective length of query: 412
Effective length of database: 368
Effective search space:   151616
Effective search space used:   151616
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 2021. 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