Alignments for a candidate for sdc in Bacillus horneckiae 1P01SC

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdc in Bacillus horneckiae 1P01SC

Align The Na+-coupled dicarboxylate (succinate; malate; fumarate) transporter, SdcL (transports aspartate, α-ketoglutarate and oxaloacetate with low affinity). Km for succinate, ~6 (characterized)
to candidate WP_083957205.1 CWS20_RS02035 DASS family sodium-coupled anion symporter

Query= TCDB::Q65NC0
         (546 letters)



>NCBI__GCF_002835735.1:WP_083957205.1
          Length = 536

 Score =  597 bits (1540), Expect = e-175
 Identities = 299/542 (55%), Positives = 394/542 (72%), Gaps = 15/542 (2%)

Query: 12  LWRSHREAKRLLLFAMPVRAGKDAGLKINSEQTMKEEKPP----SYKTP----QKIGLLL 63
           +W+ H + K+ LL         +     NSE   K  K      S+K      Q IGLLL
Sbjct: 1   MWKWHEDIKKFLLLFSAKNDSTEQDNN-NSETASKVVKQNNENNSFKQKRSKKQNIGLLL 59

Query: 64  GPALFFAVLLFFFPEGLSYEGRMVLATTLWVAVWWITEAVPIPAASLLPIVLLPLTGALE 123
           GP LF   LLF  P G+S E   VLA+TLW+A WWITEA+PIPA +LLPIVL PLTGA+ 
Sbjct: 60  GPLLFLITLLFISPPGMSGEALAVLASTLWIATWWITEAIPIPATALLPIVLFPLTGAVT 119

Query: 124 GAAVTSSYGDPIVFLFLGGFLIALAMERWNLHKRIALNIISVVGTSTSRIVLGFMAATGF 183
              VTS+Y D  +FLFLGGF+IA+AME+WNLH RIAL+IISVVGTST+++VLGFM ATGF
Sbjct: 120 -EGVTSAYADNTIFLFLGGFIIAIAMEKWNLHLRIALSIISVVGTSTTKLVLGFMIATGF 178

Query: 184 LSMWVSNTAAVMMMLPIGTAIIHQVSAVIKSERKDLAAEEAKFSKALIFSIGYAGTIGGL 243
           LSMW+SNTA  MMM+PI  A+I  V+  IK +++      ++F K+L+  I YA +IGGL
Sbjct: 179 LSMWISNTATAMMMMPIAIAVIAHVNESIKEDKES----GSRFGKSLMLGIAYAASIGGL 234

Query: 244 GTLIGTPPNIILAANIKKLYGVEVSFGGWMAFAVPVVVILLVAVWLYLTKVAHPIKMKEL 303
           GTLIGTPPN+I A  +K++YGV++SF  WM F VP   +LL   W YL K+A PI +KEL
Sbjct: 235 GTLIGTPPNMIFAGVVKEIYGVDISFATWMLFGVPFAAVLLAVAWFYLVKIAFPITIKEL 294

Query: 304 PGGKELILEEKRKLGKMSFEETMVLLVFGFAAFMWVTRTFLWDDKIPGIDDTMIAIFAAS 363
           PGGKE+I  E+++LG +SFEE +VL VF   A  W+TRTF+  + +  IDDT+IAI AA 
Sbjct: 295 PGGKEIIKSERKRLGSISFEEKLVLAVFTITALAWITRTFIPFEFMNRIDDTVIAIAAAV 354

Query: 364 LLFLIPSLNKG-GRVLDWSVSKDLPWGILLLFGGGLALATGFKETGLAEWIGGRLTVLDG 422
           +LF++PS +   G++L+W    ++PWGILLLFGGGLA+A GFK++GLA+WIG +LT+L G
Sbjct: 355 VLFILPSKSSSDGQLLNWKDGVNIPWGILLLFGGGLAIAKGFKDSGLAQWIGEQLTILQG 414

Query: 423 FNFVVIVIISTALVLFLTEITSNTATATMILPVLASLALALNVHPYALMVPAAMAANCAF 482
            + +++++  TALV FLTEITSNTATATM+ P++ASL LALN+HPYALMV A +AA+CAF
Sbjct: 415 VHLIIVILCVTALVTFLTEITSNTATATMMFPIMASLGLALNIHPYALMVAAGIAASCAF 474

Query: 483 MLPVGTPPNAIIFASGKLKISEMVRTGFVINIFTLILIVGAVFYILPHLWGVDLTVFPDN 542
           MLPV TPPNAI+F SG LKI +MV++GF ++IFT++ +   +++ +P  WG+D+T FPD 
Sbjct: 475 MLPVATPPNAIVFGSGYLKIIDMVKSGFWLSIFTILFVPVMIYFYMPIAWGIDITNFPDM 534

Query: 543 LK 544
            K
Sbjct: 535 FK 536


Lambda     K      H
   0.326    0.140    0.425 

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: 873
Number of extensions: 45
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: 546
Length of database: 536
Length adjustment: 35
Effective length of query: 511
Effective length of database: 501
Effective search space:   256011
Effective search space used:   256011
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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
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