GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Croceitalea dokdonensis DOKDO 023

Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate WP_054558634.1 I595_RS06915 dicarboxylate/amino acid:cation symporter

Query= TCDB::Q01857
         (444 letters)



>NCBI__GCF_001306415.1:WP_054558634.1
          Length = 437

 Score =  206 bits (523), Expect = 2e-57
 Identities = 131/415 (31%), Positives = 223/415 (53%), Gaps = 23/415 (5%)

Query: 22  LYVQVLVAIAAGILLGHFYPEL--GTQ-----LKPLGDAFIKLVKMIIAPVIFLTVATGI 74
           L+ Q+L+ + AG+L G    +L  G Q     ++PLG  F+KL+K+I  P+I  ++  G+
Sbjct: 6   LHWQILIGMIAGVLFGFAMNQLDWGEQFVADWIRPLGTIFVKLLKLIAIPLILASLVKGV 65

Query: 75  AGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASL------DPA 128
           + + D+ K   +  + M  ++  + +A+ IGL++ NV+QPG  +  D  S         +
Sbjct: 66  SDLKDISKFRSIGLRTMAIYMGTTLVAITIGLVLVNVIQPGVAIPADTISKLVDTYSGDS 125

Query: 129 AVATFAAKAHEQSIVG---FLTNIIPTTIVGAFADGDI-LQVLFFSVLFGIALAMVGEK- 183
            V +  A+A  Q   G   FL  ++P   V A +D  + LQV+FF++  GI++ +VG+K 
Sbjct: 126 GVTSKLAEASMQKERGPLQFLEEMVPDNAVYAMSDNSLMLQVIFFTIFLGISMLLVGQKR 185

Query: 184 GEQVVNFLNSLTAPVFKLVAILMKAAPIGAFGAMA-FTIGKYGVGSIANLAMLIGTFYIT 242
            + +  F NSL   V K+V ++M  AP+  F  +A   +       +  L    G   + 
Sbjct: 186 AKPLKKFFNSLNDVVLKMVDLIMLTAPVAVFALLASVVVSSSDPDLLLALLKYAGVVLLG 245

Query: 243 SLLFVFIVLGAVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEK-AGCKRS 301
            LL V      ++ + G+  +  L  I    LL   TSSS A LP  M ++E+  G    
Sbjct: 246 LLLMVLFYCVIISFFTGYHPLKFLIKISPAQLLAFSTSSSAATLPVTMERVEEHIGVDAE 305

Query: 302 VVGLVIPTGYSFNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITG 361
           V   V+P G + N+DGT++Y  +AA+FI+QA    L++ DQ+ ++  A+L+S G+A + G
Sbjct: 306 VSSFVLPVGATVNMDGTSLYQGVAAVFISQALAFDLTFPDQLTIVFTALLASIGSAAVPG 365

Query: 362 AGFITLAATLSVV--PSVPVA-GMALILGIDRFMSECRALTNLVGNAVATIVVAR 413
           AG + L   L  +  P+  +A G+ALI  +DR +  CR + N+ G+++  I+VA+
Sbjct: 366 AGMVMLVIVLEAIGFPADKLAIGLALIFAVDRPLDMCRTVVNVTGDSMVAILVAK 420


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: 473
Number of extensions: 28
Number of successful extensions: 7
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: 437
Length adjustment: 32
Effective length of query: 412
Effective length of database: 405
Effective search space:   166860
Effective search space used:   166860
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