Alignments for a candidate for actP in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for actP in Pseudomonas fluorescens FW300-N2E3

Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate AO353_01865 AO353_01865 cation/acetate symporter ActP

Query= SwissProt::P32705
         (549 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_01865
          Length = 552

 Score =  849 bits (2194), Expect = 0.0
 Identities = 430/551 (78%), Positives = 482/551 (87%), Gaps = 2/551 (0%)

Query: 1   MKRVLTALA-ATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRS 59
           ++R+L AL  A    A  AA+A++G V +QP N  AI+MF++FV  TL ITYWASKR +S
Sbjct: 2   IRRLLAALGIAAFAPAVWAAEALTGEVHKQPLNVSAILMFVVFVGATLCITYWASKRNKS 61

Query: 60  RSDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILF 119
            +DYY AGG ITG QNGLAIAGDYMSAASFLGISALVF SGYDGLIYS+GFLVGWPIILF
Sbjct: 62  AADYYAAGGRITGLQNGLAIAGDYMSAASFLGISALVFASGYDGLIYSIGFLVGWPIILF 121

Query: 120 LIAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGL 179
           LIAERLRNLG+YTFADVASYRL Q  IR LSACGSLVVVA YLIAQMVGAGKLI+LLFGL
Sbjct: 122 LIAERLRNLGKYTFADVASYRLGQTQIRTLSACGSLVVVAFYLIAQMVGAGKLIQLLFGL 181

Query: 180 NYHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFS 239
           +YH+AV+LVG+LM +YVLFGGMLATTWVQIIKAVLLL GASFMA MVMKHV F FN LFS
Sbjct: 182 DYHVAVILVGILMCLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVHFDFNTLFS 241

Query: 240 EAMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVF 299
           EA+ VHPKG  IM PGGLVKDPISA SLGL LMFGTAGLPHILMRFFTVSDA+EARKSV 
Sbjct: 242 EAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSVL 301

Query: 300 YATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGF 359
           YATGF+GYFYILTFIIGFGAI+LV  NP +KDA G L+GGNNMAAVHLANAVGG++FLGF
Sbjct: 302 YATGFIGYFYILTFIIGFGAILLVSTNPAFKDATGALLGGNNMAAVHLANAVGGSIFLGF 361

Query: 360 ISAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAII 418
           ISAVAFATILAVVAGLTLAGA+AVSHDLYA+V KKG A E++E+RVSKIT + LGV+AI+
Sbjct: 362 ISAVAFATILAVVAGLTLAGATAVSHDLYASVIKKGKANEKDEIRVSKITTIALGVLAIV 421

Query: 419 LGVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMIL 478
           LG+LFE+QNIAFMVGLAF+IAASCNFP++LLSMYW KLTTRGAM+GGW+GL++AV LM+L
Sbjct: 422 LGILFESQNIAFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMVGGWMGLVSAVGLMVL 481

Query: 479 GPTIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQ 538
           GPTIWVQI+GHEKAIFPYEYPALFS+ +AF+GIWFFS TD SA    ER LF  QF+RSQ
Sbjct: 482 GPTIWVQIMGHEKAIFPYEYPALFSMAIAFVGIWFFSITDKSAAADNERALFFPQFVRSQ 541

Query: 539 TGFGVEQGRAH 549
           TG G     +H
Sbjct: 542 TGLGASGAVSH 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: 1017
Number of extensions: 38
Number of successful extensions: 3
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 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)
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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