Alignments for a candidate for actP in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Pseudomonas benzenivorans DSM 8628

Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate WP_090441240.1 BLS63_RS05935 cation acetate symporter

Query= SwissProt::P32705
         (549 letters)



>NCBI__GCF_900100495.1:WP_090441240.1
          Length = 552

 Score =  840 bits (2171), Expect = 0.0
 Identities = 426/544 (78%), Positives = 477/544 (87%), Gaps = 2/544 (0%)

Query: 7   ALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSRSDYYTA 66
           AL A  P A  AA AI G V+RQP N  AI+MF+ FV  T+ ITYWASKR  S SD+YTA
Sbjct: 10  ALLAVAP-ALWAAGAIEGEVQRQPLNVSAIVMFIAFVGATMCITYWASKRNTSTSDFYTA 68

Query: 67  GGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFLIAERLR 126
           GG+I+GFQNGLAIAGDYMSAASFLGISALVF+SGYDGLIYS+GFLVGWP+ILFLIAERLR
Sbjct: 69  GGSISGFQNGLAIAGDYMSAASFLGISALVFSSGYDGLIYSIGFLVGWPVILFLIAERLR 128

Query: 127 NLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLNYHIAVV 186
           NLG+YTFADVASYRLKQ  IR LSACGSLVVVA YLIAQMVGAGKLI+LLFGL+Y++AVV
Sbjct: 129 NLGKYTFADVASYRLKQKEIRTLSACGSLVVVAFYLIAQMVGAGKLIQLLFGLDYNVAVV 188

Query: 187 LVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAVHP 246
           +VG+LM+MYVLFGGMLATTWVQIIKAVLLL GA+FMA MVMKHV F F  LFSEA+ VH 
Sbjct: 189 MVGILMVMYVLFGGMLATTWVQIIKAVLLLSGATFMAVMVMKHVNFDFGTLFSEAVKVHA 248

Query: 247 KGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFYATGFMG 306
           KG  IM PGGLVKDP+SA+SLGL LMFGTAGLPHILMRFFTVSDA+EARKSVF+ATGF+G
Sbjct: 249 KGEAIMSPGGLVKDPVSAISLGLALMFGTAGLPHILMRFFTVSDAKEARKSVFFATGFIG 308

Query: 307 YFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGFISAVAFA 366
           YFY+LTFIIGFGAI+LV  NP +KDA+G L+GGNNMAAVHLANAVGG++FLGFISAVAFA
Sbjct: 309 YFYVLTFIIGFGAILLVSTNPMFKDASGALLGGNNMAAVHLANAVGGSMFLGFISAVAFA 368

Query: 367 TILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAIILGVLFEN 425
           TILAVVAGLTLAGASAVSHDLYA+V+KKG A E++ELRVSKIT + LGV+AI LG+LFE 
Sbjct: 369 TILAVVAGLTLAGASAVSHDLYASVWKKGKANEKDELRVSKITTVALGVLAIGLGILFEK 428

Query: 426 QNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILGPTIWVQ 485
           QNIAFMVGLAF+IAASCNFP++ LSMYW  LTTRGAM+GGWLGL+TAV LMILGPT+WVQ
Sbjct: 429 QNIAFMVGLAFSIAASCNFPVLFLSMYWKNLTTRGAMLGGWLGLVTAVTLMILGPTVWVQ 488

Query: 486 ILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQTGFGVEQ 545
           +LGH +AIFPYEYPALFS+ +AF+GIWFFS TD S     ER  F  QF+RSQTGFG   
Sbjct: 489 VLGHAEAIFPYEYPALFSMAIAFVGIWFFSITDKSNSAVDERARFLPQFVRSQTGFGASG 548

Query: 546 GRAH 549
             AH
Sbjct: 549 AVAH 552


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: 1021
Number of extensions: 43
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: 552
Length adjustment: 36
Effective length of query: 513
Effective length of database: 516
Effective search space:   264708
Effective search space used:   264708
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 24 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