Aligments for a candidate for dctA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments for a candidate for dctA in Sinorhizobium meliloti 1021

Align C4-dicarboxylate transporter (substrates: fumarate, D- and L-malate, succinate, succinamide, orotate, iticonate, mesaconate) (characterized)
to candidate SM_b20611 SM_b20611 C4-dicarboxylate transporter DctA

Query= TCDB::Q01857
         (444 letters)



>FitnessBrowser__Smeli:SM_b20611
          Length = 441

 Score =  713 bits (1840), Expect = 0.0
 Identities = 368/432 (85%), Positives = 400/432 (92%)

Query: 13  KGKKPFYSHLYVQVLVAIAAGILLGHFYPELGTQLKPLGDAFIKLVKMIIAPVIFLTVAT 72
           +GK P Y HLYVQVL AIAAGILLGHFYP++GT+LKPLGDAFI+LVKMIIAPVIFLTVAT
Sbjct: 10  RGKTPLYRHLYVQVLAAIAAGILLGHFYPDIGTELKPLGDAFIRLVKMIIAPVIFLTVAT 69

Query: 73  GIAGMSDLQKVGRVAGKAMLYFLTFSTLALIIGLIVANVVQPGAGMNIDPASLDPAAVAT 132
           GIAGM+DL KVGRVAGKAM+YFL FSTLAL++GL+VANVVQPGAGM+IDPASLD  AVAT
Sbjct: 70  GIAGMTDLAKVGRVAGKAMIYFLAFSTLALVVGLVVANVVQPGAGMHIDPASLDAKAVAT 129

Query: 133 FAAKAHEQSIVGFLTNIIPTTIVGAFADGDILQVLFFSVLFGIALAMVGEKGEQVVNFLN 192
           +A KAHEQSI GFL NIIPTT+VGAFA+GDILQVLF SVLFGI+LA+VG+K E VV+FL 
Sbjct: 130 YAEKAHEQSITGFLMNIIPTTLVGAFAEGDILQVLFISVLFGISLAIVGKKAEPVVDFLQ 189

Query: 193 SLTAPVFKLVAILMKAAPIGAFGAMAFTIGKYGVGSIANLAMLIGTFYITSLLFVFIVLG 252
           +LT P+F+LVAILMKAAPIGAFGAMAFTIGKYG+ SIANLAMLIGTFY+TS LFVFIVLG
Sbjct: 190 ALTLPIFRLVAILMKAAPIGAFGAMAFTIGKYGIASIANLAMLIGTFYLTSFLFVFIVLG 249

Query: 253 AVARYNGFSIVALLRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYS 312
           AVARYNGFSI++L+RYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYS
Sbjct: 250 AVARYNGFSILSLIRYIKEELLLVLGTSSSEAALPGLMNKMEKAGCKRSVVGLVIPTGYS 309

Query: 313 FNLDGTNIYMTLAALFIAQATGIHLSWGDQILLLLVAMLSSKGAAGITGAGFITLAATLS 372
           FNLDGTNIYMTLAALFIAQAT   LS+GDQILLLLVAMLSSKGAAGITGAGFITLAATLS
Sbjct: 310 FNLDGTNIYMTLAALFIAQATDTPLSYGDQILLLLVAMLSSKGAAGITGAGFITLAATLS 369

Query: 373 VVPSVPVAGMALILGIDRFMSECRALTNLVGNAVATIVVARWENELDTVQLAAALGGQTG 432
           VVPSVPVAGMALILGIDRFMSECRALTN VGNAVATIVVA+WE ELD  QL+AALGG+  
Sbjct: 370 VVPSVPVAGMALILGIDRFMSECRALTNFVGNAVATIVVAKWEGELDQAQLSAALGGEAS 429

Query: 433 EDTSAAGLQPAE 444
            +   A +QPAE
Sbjct: 430 VEAIPAVVQPAE 441


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: 763
Number of extensions: 30
Number of successful extensions: 1
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: 441
Length adjustment: 32
Effective length of query: 412
Effective length of database: 409
Effective search space:   168508
Effective search space used:   168508
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 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 paper from 2022 on GapMind for carbon sources, or view the source code.

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