Alignments for a candidate for actP in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Pseudomonas fluorescens GW456-L13

Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate PfGW456L13_2421 Acetate permease ActP (cation/acetate symporter)

Query= SwissProt::P32705
         (549 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2421
          Length = 548

 Score =  738 bits (1906), Expect = 0.0
 Identities = 368/550 (66%), Positives = 445/550 (80%), Gaps = 3/550 (0%)

Query: 1   MKRVLTALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSR 60
           M R+L      L    + A A  GA   +P NW AI MFL+FV+FTLG+T WA+ R RS 
Sbjct: 1   MNRLLALFLLPLAAVTDVAMAADGA--SRPLNWNAIGMFLVFVLFTLGVTRWAALRTRST 58

Query: 61  SDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFL 120
           SD+YTAGG +TGFQNGLAIAGD +SAASFLGISA++F +GYDGL+Y+LG L GWPIILFL
Sbjct: 59  SDFYTAGGGMTGFQNGLAIAGDMISAASFLGISAMMFLNGYDGLLYALGVLAGWPIILFL 118

Query: 121 IAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLN 180
           IAERLRNLG+YTFADV SYRL+Q P+R+ SA G+L V  +YL+AQMVGAGKLIELLFG++
Sbjct: 119 IAERLRNLGKYTFADVVSYRLEQTPVRLTSAFGTLTVALMYLVAQMVGAGKLIELLFGID 178

Query: 181 YHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSE 240
           Y  AV+LVGVLM+ YV FGGMLATTWVQIIKAV+LLFG SFMAFMV+KH GFS   +F+ 
Sbjct: 179 YLYAVMLVGVLMVFYVTFGGMLATTWVQIIKAVMLLFGTSFMAFMVLKHFGFSTEAMFAG 238

Query: 241 AMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFY 300
           A AVH KG  IM PGGL+ +PI A+SLGLG+MFGTAGLPHILMRFFTVSDA+EARKSVFY
Sbjct: 239 ATAVHAKGNAIMAPGGLLSNPIDAISLGLGMMFGTAGLPHILMRFFTVSDAKEARKSVFY 298

Query: 301 ATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGFI 360
           ATGF+GYFY+L  I+GFGAI++VG +P ++DA+G +IGG NM AVHLA+AVGGNLFLGFI
Sbjct: 299 ATGFIGYFYLLLIIVGFGAIVMVGTDPAFRDASGAIIGGGNMVAVHLAHAVGGNLFLGFI 358

Query: 361 SAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAIIL 419
           SAVAFATILAVVAGL L+GASAVSHDLYA V +KG A+E++E+RVS+I  L +GV+AI+L
Sbjct: 359 SAVAFATILAVVAGLALSGASAVSHDLYACVMRKGQASEQQEMRVSRIATLCIGVLAIVL 418

Query: 420 GVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILG 479
           G+LFE+QNIAF+ GL  AIAAS NFP++ LSMYW  LTTRGA++G   GL++A+VL++L 
Sbjct: 419 GLLFESQNIAFLSGLVLAIAASVNFPVLFLSMYWKGLTTRGAVLGSLSGLVSAIVLLVLS 478

Query: 480 PTIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQT 539
           P +WV ++ H+KA+FPY  PALFS+++AF   W FS TD S   A ER  + AQFIRS T
Sbjct: 479 PAVWVNVMHHDKALFPYSNPALFSMSLAFFSAWLFSVTDTSPRAALERGRYLAQFIRSMT 538

Query: 540 GFGVEQGRAH 549
           G G      H
Sbjct: 539 GIGATGASKH 548


Lambda     K      H
   0.329    0.142    0.424 

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: 983
Number of extensions: 49
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: 549
Length of database: 548
Length adjustment: 36
Effective length of query: 513
Effective length of database: 512
Effective search space:   262656
Effective search space used:   262656
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 (21.8 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
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