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 Acetate permease ActP-2/ActP2/ActP3 (characterized)
to candidate Dsui_0290 Dsui_0290 SSS sodium solute transporter

Query= TCDB::D5APM1
         (578 letters)



>FitnessBrowser__PS:Dsui_0290
          Length = 582

 Score =  808 bits (2088), Expect = 0.0
 Identities = 430/585 (73%), Positives = 479/585 (81%), Gaps = 21/585 (3%)

Query: 8   TRLAAVSALSLTPGLALAAGAIEGAVQKQPTNWTAIAMFGFFVVATLFITKWAAGRTKSA 67
           T   A++ L L      AA A+EG  +KQ TNWTAI MFG FV+ATL+ITKWAA +TK+A
Sbjct: 5   TNTLALAGLGLLSSPVFAA-ALEGQAEKQATNWTAIIMFGAFVLATLWITKWAASKTKTA 63

Query: 68  ADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVMLQGYDGLIYSIGFLVGWPILTFL 127
           ADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAV   GYDGLIYSIGFLVGWPI+ FL
Sbjct: 64  ADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVFANGYDGLIYSIGFLVGWPIIMFL 123

Query: 128 MAERLRNLGKFTFADVAAFPFAQTPVRVFAAMSTLVVVAFYLIAQMVGAGQLIKLLFGLE 187
           MAERLRNLGKFTFADVAA+ F  TP+R  AA  TLVVVAFYLIAQMVGAGQLIKLLFGL+
Sbjct: 124 MAERLRNLGKFTFADVAAYRFQATPIRALAASGTLVVVAFYLIAQMVGAGQLIKLLFGLD 183

Query: 188 YLYAVIVVGILMMVYVLFGGMTATTWVQIIKACLLLGGASFMALMVMVHYGFSLESLFAD 247
           Y  AV++VGILMMVYVLFGGMTATTWVQIIKA LLL GASFM  MV+  YGFS E+LFAD
Sbjct: 184 YWMAVVLVGILMMVYVLFGGMTATTWVQIIKAVLLLSGASFMVFMVLAKYGFSPEALFAD 243

Query: 248 SVKVKTDLAL-------------AAGKTPEEAAAA-GISIMGPGTFVKDPISAISFGMAL 293
           +V++KTDLA              A  +T   AAAA G SIMGPG+F+KDPISAISFGMAL
Sbjct: 244 AVRIKTDLAAKGLLAKALETDPSATAETVAAAAAAKGQSIMGPGSFIKDPISAISFGMAL 303

Query: 294 MFGTAGLPHILMRFFTVPSAKEARKSVMWATVWIGYFYMLTFIIGFGAIVYVLTNPGLVS 353
           MFGTAGLPHILMRFFTVP  KEARKSV WAT WIGYFY+LTFIIGFGAIV V TNP  + 
Sbjct: 304 MFGTAGLPHILMRFFTVPDGKEARKSVFWATTWIGYFYILTFIIGFGAIVLVGTNPEFL- 362

Query: 354 YDAKGALTLVGGNNMAAIHLAQAVGGNIFLGFISAVAFATILAVVAGLTLSGASAVSHDL 413
            DAKG L   GG NMAAIHLA AVGGN+FLGFISAVAFATILAVVAGLTLSGASAVSHDL
Sbjct: 363 -DAKGVLK--GGGNMAAIHLANAVGGNVFLGFISAVAFATILAVVAGLTLSGASAVSHDL 419

Query: 414 YSTVFKNGKADSASELRVSRITTICLGIVAVVLGLAFEKQNIAFMVSLAFAIAASANFPV 473
           Y++VF++G  DSA+E+RVS++TT+ LGI+AVVLG+AFEKQNIAFMVSLAFAIAASANFPV
Sbjct: 420 YASVFRHGNVDSATEMRVSKMTTVALGIIAVVLGIAFEKQNIAFMVSLAFAIAASANFPV 479

Query: 474 LFMSLLWKGMTTRGAVIGGSLGLISSVALTVISPSVWEATLGFEKGSAPFPYTSPALFSM 533
           LFMS+LWK  TT+GA  GG LGLI++V LTV+S S+W   LG    +  FPY SPALFSM
Sbjct: 480 LFMSVLWKDCTTKGAFYGGFLGLITAVVLTVLSKSIWVDILG--NKTEIFPYASPALFSM 537

Query: 534 VLGFAGIWLFSITDKSRRGDQDRDGYLAQEIRSETGIGAAEASAH 578
             GF GIWLFS+ D+S +  ++R  YL QEIRSETGIGAA AS+H
Sbjct: 538 AAGFIGIWLFSLMDRSEQAAKERVAYLDQEIRSETGIGAAAASSH 582


Lambda     K      H
   0.326    0.138    0.405 

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: 1220
Number of extensions: 53
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: 578
Length of database: 582
Length adjustment: 36
Effective length of query: 542
Effective length of database: 546
Effective search space:   295932
Effective search space used:   295932
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 (21.7 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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, 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