Alignments for a candidate for actP in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Dechlorosoma suillum PS

Align Cation acetate symporter (characterized, see rationale)
to candidate Dsui_0290 Dsui_0290 SSS sodium solute transporter

Query= uniprot:A0A165ZRB0
         (552 letters)



>FitnessBrowser__PS:Dsui_0290
          Length = 582

 Score =  728 bits (1879), Expect = 0.0
 Identities = 380/576 (65%), Positives = 446/576 (77%), Gaps = 30/576 (5%)

Query: 6   LALLSIAAFAPGAWAAEALTGAVQKQPLNVAAILMFVAFVGATLYITYWASKKNNSAADY 65
           LAL  +   +   +AA AL G  +KQ  N  AI+MF AFV ATL+IT WA+ K  +AAD+
Sbjct: 8   LALAGLGLLSSPVFAA-ALEGQAEKQATNWTAIIMFGAFVLATLWITKWAASKTKTAADF 66

Query: 66  YAAGGKITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPIILFLIAE 125
           Y AGG ITGFQNGLAIAGDYMSAASFLGISA VF +GYDGLIYSIGFLVGWPII+FL+AE
Sbjct: 67  YTAGGGITGFQNGLAIAGDYMSAASFLGISAAVFANGYDGLIYSIGFLVGWPIIMFLMAE 126

Query: 126 RLRNLGKYTFADVASYRLGQTQIRSLSASGSLVVVAFYLIAQMVGAGKLIQLLFGLDYHV 185
           RLRNLGK+TFADVA+YR   T IR+L+ASG+LVVVAFYLIAQMVGAG+LI+LLFGLDY +
Sbjct: 127 RLRNLGKFTFADVAAYRFQATPIRALAASGTLVVVAFYLIAQMVGAGQLIKLLFGLDYWM 186

Query: 186 AVILVGILMCLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNMLFAEAVK 245
           AV+LVGILM +YVLFGGM ATTWVQIIKAVLLLSGASFM  MV+    F    LFA+AV+
Sbjct: 187 AVVLVGILMMVYVLFGGMTATTWVQIIKAVLLLSGASFMVFMVLAKYGFSPEALFADAVR 246

Query: 246 VHP-----------------------------KGEAIMSPGGLVKDPISAFSLGLALMFG 276
           +                               KG++IM PG  +KDPISA S G+ALMFG
Sbjct: 247 IKTDLAAKGLLAKALETDPSATAETVAAAAAAKGQSIMGPGSFIKDPISAISFGMALMFG 306

Query: 277 TAGLPHILMRFFTVSDAKEARKSVLYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAG 336
           TAGLPHILMRFFTV D KEARKSV +AT +IGYFYILTFIIGFGAI+LV TNP F DA G
Sbjct: 307 TAGLPHILMRFFTVPDGKEARKSVFWATTWIGYFYILTFIIGFGAIVLVGTNPEFLDAKG 366

Query: 337 ALLGGNNMAAVHLANAVGGSIFLGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIRK 396
            L GG NMAA+HLANAVGG++FLGFISAVAFATILAVVAGLTL+GASAVSHDLYASV R 
Sbjct: 367 VLKGGGNMAAIHLANAVGGNVFLGFISAVAFATILAVVAGLTLSGASAVSHDLYASVFRH 426

Query: 397 GRVNEKDEIRVSKITTIALAVLAITLGILFEKQNIAFMVGLAFSIAASCNFPVLLLSMYW 456
           G V+   E+RVSK+TT+AL ++A+ LGI FEKQNIAFMV LAF+IAAS NFPVL +S+ W
Sbjct: 427 GNVDSATEMRVSKMTTVALGIIAVVLGIAFEKQNIAFMVSLAFAIAASANFPVLFMSVLW 486

Query: 457 KKLTTRGAMIGGWLGLVSAVGLMILGPTIWVQIMGHEKAIFPYEYPALFSMAIAFVGIWF 516
           K  TT+GA  GG+LGL++AV L +L  +IWV I+G++  IFPY  PALFSMA  F+GIW 
Sbjct: 487 KDCTTKGAFYGGFLGLITAVVLTVLSKSIWVDILGNKTEIFPYASPALFSMAAGFIGIWL 546

Query: 517 FSITDKSAEGANERALFFPQFVRSQTGLGASGAVNH 552
           FS+ D+S + A ER  +  Q +RS+TG+GA+ A +H
Sbjct: 547 FSLMDRSEQAAKERVAYLDQEIRSETGIGAAAASSH 582


Lambda     K      H
   0.328    0.140    0.414 

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: 1015
Number of extensions: 45
Number of successful extensions: 2
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: 552
Length of database: 582
Length adjustment: 36
Effective length of query: 516
Effective length of database: 546
Effective search space:   281736
Effective search space used:   281736
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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 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