Alignments for a candidate for sdcL in Bacillus horneckiae 1P01SC

GapMind for catabolism of small carbon sources

Alignments for a candidate for sdcL 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_066193458.1 CWS20_RS13065 SLC13 family permease

Query= TCDB::Q65NC0
         (546 letters)



>NCBI__GCF_002835735.1:WP_066193458.1
          Length = 549

 Score =  555 bits (1429), Expect = e-162
 Identities = 280/549 (51%), Positives = 382/549 (69%), Gaps = 5/549 (0%)

Query: 1   MKSSVVSAWDMLWRSHREAKRLLLFA----MPVRAGKDAGLKINSEQTMKEEKPPSYKTP 56
           M+ S+ +    LW SH+ +K L+ FA    +   + K++     S+   K+ + P+Y   
Sbjct: 1   MEKSLRTWSQSLWLSHQRSKDLITFASLRKVKTESPKESVDAAVSDGGNKQNEKPAYTKS 60

Query: 57  QKIGLLLGPALFFAVLLFFFPEGLSYEGRMVLATTLWVAVWWITEAVPIPAASLLPIVLL 116
           Q +GLLLGP LF   +      GLS EGR VLA TLWV+ WWI EA+P+   SLLPIVLL
Sbjct: 61  QFVGLLLGPLLFLMTVFLLPLPGLSEEGRAVLAITLWVSTWWILEAMPLGITSLLPIVLL 120

Query: 117 PLTGALEGAAVTSSYGDPIVFLFLGGFLIALAMERWNLHKRIALNIISVVGTSTSRIVLG 176
           PL G + GA  T+SYGDP +FLFLGGF IALA+E+W LH+RIAL IIS VGTSTS +V G
Sbjct: 121 PLMGTITGAQATASYGDPNIFLFLGGFAIALALEKWKLHERIALTIISFVGTSTSGLVYG 180

Query: 177 FMAATGFLSMWVSNTAAVMMMLPIGTAIIHQVSAVIKSERKDLAAEEAKFSKALIFSIGY 236
           FM ATGFLSMW+SN A VMMM+PIGTAI  +V  ++K E      E+ KF+K+++FSIG+
Sbjct: 181 FMFATGFLSMWISNVATVMMMIPIGTAIAFKVVELMKKEGTYTLEEDKKFTKSIVFSIGF 240

Query: 237 AGTIGGLGTLIGTPPNIILAANIKKLYGVEVSFGGWMAFAVPVVVILLVAVWLYLTKVAH 296
            G IGG  TLIGTPPN+ILA  IK++YG+E+SF  W  FA P+++IL V    YLTK+A+
Sbjct: 241 GGIIGGSATLIGTPPNLILAGLIKEMYGIEISFAKWFLFAFPLILILAVFAAFYLTKIAY 300

Query: 297 PIKMKELPGGKELILEEKRKLGKMSFEETMVLLVFGFAAFMWVTRTFLWDDKIPGIDDTM 356
           P+K+K L  G++ +L+EK+ LGKM++EE +V +VF   AFMW+TR+F+W D IPGI DTM
Sbjct: 301 PMKVKRLEHGRQFVLDEKQALGKMTYEEKIVSIVFSLTAFMWLTRSFIWTDIIPGISDTM 360

Query: 357 IAIFAASLLFLIPSLNK-GGRVLDWSVSKDLPWGILLLFGGGLALATGFKETGLAEWIGG 415
           IA+  A LL+LIP+  K GGR+L+    K +PW +LLL GGGLA+A GF  T L+ WIG 
Sbjct: 361 IAMTGAILLYLIPASKKNGGRILESDSLKHMPWDVLLLVGGGLAIAAGFSGTDLSTWIGS 420

Query: 416 RLTVLDGFNFVVIVIISTALVLFLTEITSNTATATMILPVLASLALALNVHPYALMVPAA 475
           +L +L+G  +++I+ I+T L + +T+I  NTA  T+ +P+ A+LALA++ HP  LM  AA
Sbjct: 421 QLLLLEGTPYILILSITTILTIGITQIAPNTAITTIFVPIAATLALAIDAHPLPLMAAAA 480

Query: 476 MAANCAFMLPVGTPPNAIIFASGKLKISEMVRTGFVINIFTLILIVGAVFYILPHLWGVD 535
           + A  AFMLP+GTP  AIIF +GK+ I +M+R G  I I   ILI+  ++++ P ++ ++
Sbjct: 481 LGAGFAFMLPIGTPSQAIIFGTGKVTIMDMLRKGTWITILATILIITFIYFLFPIVFDLN 540

Query: 536 LTVFPDNLK 544
           L  FP  LK
Sbjct: 541 LLEFPSELK 549


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: 874
Number of extensions: 49
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: 546
Length of database: 549
Length adjustment: 36
Effective length of query: 510
Effective length of database: 513
Effective search space:   261630
Effective search space used:   261630
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: 53 (25.0 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)
Organisms (tab-delimited)
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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 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