Aligments for a candidate for actP in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for actP in Cupriavidus basilensis 4G11

Align Cation acetate symporter (characterized, see rationale)
to candidate RR42_RS06400 RR42_RS06400 acetate permease

Query= uniprot:A0A165ZRB0
         (552 letters)



>FitnessBrowser__Cup4G11:RR42_RS06400
          Length = 546

 Score =  709 bits (1830), Expect = 0.0
 Identities = 361/533 (67%), Positives = 429/533 (80%), Gaps = 1/533 (0%)

Query: 12  AAFAPGAWAAEALTGAVQKQPLNVAAILMFVAFVGATLYITYWASKKNNSAADYYAAGGK 71
           AA    A  A A  G+V  Q +NV AI MF+ FV ATL +T WA++ N+S AD+YAAGGK
Sbjct: 11  AALLLTALPAFAAPGSVG-QGMNVIAIAMFLMFVAATLVVTRWAARSNHSVADHYAAGGK 69

Query: 72  ITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPIILFLIAERLRNLG 131
           IT  QNG AIAGDYMSAAS LGISALVFTSGYDGLIYSIGFL  WPIILFLIAE LRNLG
Sbjct: 70  ITALQNGWAIAGDYMSAASLLGISALVFTSGYDGLIYSIGFLASWPIILFLIAEPLRNLG 129

Query: 132 KYTFADVASYRLGQTQIRSLSASGSLVVVAFYLIAQMVGAGKLIQLLFGLDYHVAVILVG 191
           ++T ADV SYRL Q  IR+ SAS S+V+V  YL++QMVGAGKL++LLFG  Y  AV+LVG
Sbjct: 130 RFTLADVVSYRLRQRPIRAFSASSSIVIVLLYLVSQMVGAGKLVELLFGFSYTAAVVLVG 189

Query: 192 ILMCLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNMLFAEAVKVHPKGE 251
           +LM +YV FGGMLATTW+QIIKAVLLL+GA+FMA MVM    F  N LFA+A++ H K  
Sbjct: 190 VLMVVYVFFGGMLATTWIQIIKAVLLLAGAAFMAFMVMSRFGFSLNALFAQAIEAHGKHA 249

Query: 252 AIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSVLYATGFIGYFY 311
           AIM PGGLV DP+SA SLGLAL+FGTAGLPHILMRFFTV D K ARKS+LYATG +G  Y
Sbjct: 250 AIMRPGGLVSDPVSAVSLGLALIFGTAGLPHILMRFFTVGDVKAARKSILYATGIVGIGY 309

Query: 312 ILTFIIGFGAILLVSTNPAFKDAAGALLGGNNMAAVHLANAVGGSIFLGFISAVAFATIL 371
            L  IIGFG I LV+++PA+   AGA++GG NM AVHLA+AVGG++FLGFI AVAF+TIL
Sbjct: 310 ALIIIIGFGTIALVASDPAYHTPAGAVIGGVNMVAVHLAHAVGGNLFLGFICAVAFSTIL 369

Query: 372 AVVAGLTLAGASAVSHDLYASVIRKGRVNEKDEIRVSKITTIALAVLAITLGILFEKQNI 431
           AVVAGLTLAG+SA+SHDLYA V+R+G   +K+E+RVS++TT+ L VL+I LGILFEKQ I
Sbjct: 370 AVVAGLTLAGSSAISHDLYAKVLRQGNATDKEEMRVSRMTTLVLGVLSILLGILFEKQTI 429

Query: 432 AFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMIGGWLGLVSAVGLMILGPTIWVQIMG 491
           AF+V L FSIAAS NFPVLLLS+YW+ LTTRGA++GG LGL+SAV L +L PT+WVQ++G
Sbjct: 430 AFIVSLTFSIAASSNFPVLLLSIYWRGLTTRGAVVGGSLGLLSAVVLTVLSPTVWVQVLG 489

Query: 492 HEKAIFPYEYPALFSMAIAFVGIWFFSITDKSAEGANERALFFPQFVRSQTGL 544
           H +AI+PYEYPALFSM +AF GI+ FS+TD+SA GA ER  F  Q V  + GL
Sbjct: 490 HARAIYPYEYPALFSMLVAFAGIYVFSVTDRSARGARERGAFNNQLVDCELGL 542


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: 901
Number of extensions: 48
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: 552
Length of database: 546
Length adjustment: 36
Effective length of query: 516
Effective length of database: 510
Effective search space:   263160
Effective search space used:   263160
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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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