Alignments for a candidate for actP in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Pseudomonas stutzeri RCH2

Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate GFF2882 Psest_2938 transporter, SSS family

Query= SwissProt::P32705
         (549 letters)



>FitnessBrowser__psRCH2:GFF2882
          Length = 551

 Score =  808 bits (2087), Expect = 0.0
 Identities = 406/550 (73%), Positives = 471/550 (85%), Gaps = 2/550 (0%)

Query: 1   MKRVLTALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSR 60
           ++ ++TAL   +   A  ADAI+G VE+Q TN+ AIIMF++F+ FT+GIT WA+KR  S 
Sbjct: 3   LRFLMTALLLAVS-PALLADAITGEVEKQATNYTAIIMFVVFIAFTMGITKWAAKRNTST 61

Query: 61  SDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFL 120
           +DYYTAGG+ITGFQNGLAIAGD+MSAASFLGISALV+TSGYDGLIYS+GFLVGWPIILFL
Sbjct: 62  ADYYTAGGSITGFQNGLAIAGDFMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIILFL 121

Query: 121 IAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLN 180
           +AERLRNLG++TF+DVASYRL Q  IR+LSA GSL+VVA YLIAQMVGAGKLI+LLFGL+
Sbjct: 122 MAERLRNLGKFTFSDVASYRLGQTQIRLLSAFGSLIVVAFYLIAQMVGAGKLIQLLFGLD 181

Query: 181 YHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSE 240
           Y++AVVLVGVLM+MYVLFGGMLATTWVQIIKAVLLL GASFMA MVMK VGF F +LF+E
Sbjct: 182 YYVAVVLVGVLMVMYVLFGGMLATTWVQIIKAVLLLSGASFMAIMVMKSVGFDFGSLFAE 241

Query: 241 AMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFY 300
           A+ +H KG  IM PGGLV DPISA+SLGL LMFGTAGLPHILMRFFTVSDA+EARKSVFY
Sbjct: 242 AVKIHEKGAQIMSPGGLVSDPISAISLGLALMFGTAGLPHILMRFFTVSDAKEARKSVFY 301

Query: 301 ATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGFI 360
           ATGF+GYFYILTFIIGFGAI+LV  NPE+KD  G ++GG NM A+HLA+AVGGNLFLGFI
Sbjct: 302 ATGFIGYFYILTFIIGFGAILLVSTNPEFKDVTGAIVGGTNMVAIHLASAVGGNLFLGFI 361

Query: 361 SAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAIIL 419
           SAVAFATILAVVAGLTLAGASAVSHDLYA V K+G A E +E+RV+K+T L LGV+AI+L
Sbjct: 362 SAVAFATILAVVAGLTLAGASAVSHDLYACVIKQGKAREEDEMRVTKLTTLTLGVVAILL 421

Query: 420 GVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMILG 479
           G++FE QNIAFMVGLAF+IAASCNFP++ LSMYW  L+TRGA+ GG LGL TA++L I+ 
Sbjct: 422 GIIFEKQNIAFMVGLAFSIAASCNFPVLFLSMYWKGLSTRGALFGGSLGLFTALLLTIIS 481

Query: 480 PTIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQT 539
           PT+WV + G  +AIFPY+YPALFS+  AF GIWFFS TD S     ERE F AQF+RSQT
Sbjct: 482 PTVWVDVFGFAEAIFPYKYPALFSMAAAFAGIWFFSVTDKSKRAGEERERFFAQFVRSQT 541

Query: 540 GFGVEQGRAH 549
           G G     AH
Sbjct: 542 GLGATGAVAH 551


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: 1028
Number of extensions: 39
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: 551
Length adjustment: 36
Effective length of query: 513
Effective length of database: 515
Effective search space:   264195
Effective search space used:   264195
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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