GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Flavobacterium beibuense F44-8

Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate WP_035131390.1 Q763_RS03785 cation:dicarboxylase symporter family transporter

Query= TCDB::Q01857
         (444 letters)



>NCBI__GCF_000769915.1:WP_035131390.1
          Length = 470

 Score =  296 bits (758), Expect = 9e-85
 Identities = 163/395 (41%), Positives = 241/395 (61%), Gaps = 8/395 (2%)

Query: 26  VLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVATGIAGMSDLQKVGR 85
           +LV +  G  +GH +PE G  L+ L   F+KL+K I+ P+IF T+  GIAG S++++VGR
Sbjct: 61  ILVCLVIGAAIGHEWPEAGQGLQVLSKIFLKLIKTIVGPLIFATLVYGIAGHSNIKQVGR 120

Query: 86  VAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVATFAAKAHEQSIVGF 145
           +  K++LYF   +TLAL IGL   N+ + G G+      + P  +      A  Q+    
Sbjct: 121 MGWKSLLYFEIVTTLALFIGLAAINITKAGEGI------IQPTDIKETIQAAEPQTWQQI 174

Query: 146 LTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQV-VNFLNSLTAPVFKLVAI 204
           + +I P  I  + A+G++LQ++ FSV+FGIAL MV EK  +V V+F  SL+  +FK   I
Sbjct: 175 ILHIFPENIAKSMAEGEVLQIVVFSVIFGIALIMVPEKKRKVMVDFTQSLSEVMFKFTNI 234

Query: 205 LMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLGAVARYNGFSIVA 264
           +M  APIG   AMA+T+G  G+  +  L  L+ T Y   L+FV IV   +A +    + A
Sbjct: 235 VMYFAPIGVGAAMAYTVGHMGLSVLIPLLKLLLTLYGALLVFVIIVFIPIALFIKLDLRA 294

Query: 265 LLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYSFNLDGTNIYMTL 324
            ++ I E + +   T+SSEAALP  M  ME  G  R +V  V+P GYSFNLDGT +Y++L
Sbjct: 295 FIKAIGEPVSIAFATTSSEAALPRAMEAMESIGVPRKIVSFVMPMGYSFNLDGTTLYLSL 354

Query: 325 AALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLSVVPSVPVAGMAL 384
           A++F+AQA GI LS G+Q++++   M++SKG AGI  A  + L  T +   ++PV  + +
Sbjct: 355 ASVFVAQAAGIDLSIGEQLIMVFTLMVTSKGVAGIPRASLVILMGTAASF-NLPVWPIFI 413

Query: 385 ILGIDRFMSECRALTNLVGNAVATIVVARWENELD 419
           ILGID  M   R   N+VGN +A+ V+A+WE E D
Sbjct: 414 ILGIDELMDMARTSINVVGNCLASAVIAKWEGEFD 448


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: 483
Number of extensions: 22
Number of successful extensions: 4
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: 470
Length adjustment: 33
Effective length of query: 411
Effective length of database: 437
Effective search space:   179607
Effective search space used:   179607
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: 51 (24.3 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