Alignments for a candidate for dctA in Williamsia sterculiae CPCC 203464

GapMind for catabolism of small carbon sources

Alignments for a candidate for dctA in Williamsia sterculiae CPCC 203464

Align Fumarate:H+ symporter of 442 aas and 14 established TMSs, DctA. Responsible for the transport of dicarboxylates such as succinate, fumarate, and malate (characterized)
to candidate WP_076479959.1 BW971_RS12205 C4-dicarboxylate transporter DctA

Query= TCDB::Q1J1H5
         (442 letters)



>NCBI__GCF_900156495.1:WP_076479959.1
          Length = 457

 Score =  429 bits (1102), Expect = e-124
 Identities = 225/422 (53%), Positives = 308/422 (72%), Gaps = 7/422 (1%)

Query: 5   FRSLYVQVLIAIVLGILVGFLFPSFGEGLKPLGDGFIKLIKMLIAPIIFATVVSGIAHMR 64
           + SL++Q+L+AIV GI+VG+L+P  G  +KPL DGFIKLIKMLIAPIIF TVV GIAH+ 
Sbjct: 22  YTSLFLQLLVAIVAGIMVGWLWPDLGSNVKPLADGFIKLIKMLIAPIIFCTVVLGIAHVG 81

Query: 65  DTKKVGRVGGKALIYFEVVTTFALVIGLVVANILKPGHGMNVNPATL--DTSAISKYTQA 122
           D K VGR+G KALIYFE VTTFAL+ GLVV NI+KPG G +V+PATL     A++K T+ 
Sbjct: 82  DLKAVGRIGVKALIYFEAVTTFALLFGLVVGNIVKPGAGFSVDPATLAGGADAVAKKTED 141

Query: 123 AGEQSVADFLLHIIPNTLVSAFTEGDLLQVLLISVLFGFALTQLGTLGQKV-LAGIEAVN 181
                  +FLL IIP ++ SAF E  LLQVL  +VLFG AL +LG  G  V L  ++ ++
Sbjct: 142 GELPHTVEFLLSIIPTSVFSAFAENALLQVLFFAVLFGLALAKLGEKGPPVVLELVDHLS 201

Query: 182 SAVFVILGFVMRLAPIGAFGAMAFTIGKYGVGTLAQLAYLMVAFYATCLLFVFVVLGLIA 241
           +  F I+G++MRLAP+GAFGAMA+ IG+YG+G+LA    L+ A Y   +LF+ ++LG +A
Sbjct: 202 NIFFTIIGWIMRLAPLGAFGAMAYIIGQYGIGSLASYGKLIGACYLAAVLFI-LILGAVA 260

Query: 242 RF-AGFSILKFIRFIKEELLLVLGTSSSESALPRLITKLEYAGANRSVVGLVVPAGYSFN 300
            F AG ++ +F+ +IK+E+ L LGT+S+E  LPR++TKL  AG +R+  GLV+P GYSFN
Sbjct: 261 WFLAGVNLWRFLVYIKDEVFLALGTASTEVVLPRIMTKLNNAGCSRTTTGLVIPTGYSFN 320

Query: 301 LDGTSIYLTMATLFIAQATNTHLSLGQQLGILGVLLLTSKGAAGVTGSGFITLAATLSAV 360
           LDG ++YL++  LF+AQA    LS+G+Q+  + +L+LTSKG AGV GS F+ L+AT++A+
Sbjct: 321 LDGATLYLSICILFLAQALGVDLSIGEQITAVLILMLTSKGMAGVPGSSFLALSATVAAI 380

Query: 361 GH--VPVAGLALILGIDRFMSEARALTNFVGNGVATLVIARSEKALDTNRLQRVLNGEVL 418
           GH  +PVA +AL+LG DR M   R   N +GN +AT V+A  E  LD +R++RVL+GE +
Sbjct: 381 GHGAIPVAAVALLLGADRIMDSMRVSVNLLGNCIATFVVANWEGQLDKDRMRRVLSGEYV 440

Query: 419 PP 420
           PP
Sbjct: 441 PP 442


Lambda     K      H
   0.325    0.142    0.398 

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: 524
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: 442
Length of database: 457
Length adjustment: 33
Effective length of query: 409
Effective length of database: 424
Effective search space:   173416
Effective search space used:   173416
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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources