Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate GFF1743 PS417_08865 acetate permease
Query= SwissProt::P32705 (549 letters) >FitnessBrowser__WCS417:GFF1743 Length = 552 Score = 847 bits (2188), Expect = 0.0 Identities = 430/551 (78%), Positives = 485/551 (88%), Gaps = 2/551 (0%) Query: 1 MKRVLTALAATL-PFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRS 59 ++R+L L A++ A AADA++G V +QP N AI+MF++FV TL ITYWASKR +S Sbjct: 2 IRRLLAILGASIFAPAVWAADALTGEVHKQPLNVSAIVMFVVFVGATLCITYWASKRNKS 61 Query: 60 RSDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILF 119 +DYY AGG ITGFQNGLAIAGDYMSAASFLGISALV+TSGYDGLIYS+GFLVGWPIILF Sbjct: 62 AADYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIILF 121 Query: 120 LIAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGL 179 LIAERLRNLG+YTFADVASYRL Q IR LSACGSLVVVA YLIAQMVGAGKLI+LLFGL Sbjct: 122 LIAERLRNLGKYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFGL 181 Query: 180 NYHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFS 239 +YH+AV+LVG+LM++YVLFGGMLATTWVQIIKAVLLL GASFMA MVMKHV F FN LFS Sbjct: 182 DYHVAVILVGILMVLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALFS 241 Query: 240 EAMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVF 299 EA+ VHPKG IM PGGLVKDPISA SLGL LMFGTAGLPHILMRFFTVSDA+EARKSVF Sbjct: 242 EAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSVF 301 Query: 300 YATGFMGYFYILTFIIGFGAIMLVGANPEYKDAAGHLIGGNNMAAVHLANAVGGNLFLGF 359 YATGF+GYFYILTFIIGFGAI+LV NP +KDAAG L+GGNNMAAVHLANAVGG++FLGF Sbjct: 302 YATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALMGGNNMAAVHLANAVGGSIFLGF 361 Query: 360 ISAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLILGVIAII 418 ISAVAFATILAVVAGLTLAGASAVSHDLYA+V KKG A +++E+RVSKIT + LGV+AI Sbjct: 362 ISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANDKDEIRVSKITTIALGVLAIG 421 Query: 419 LGVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITAVVLMIL 478 LG+LFE+QNIAFMVGLAF+IAASCNFP++LLSMYW LTTRGAM+GGWLGL++AV LM+L Sbjct: 422 LGILFESQNIAFMVGLAFSIAASCNFPVLLLSMYWKNLTTRGAMIGGWLGLVSAVGLMVL 481 Query: 479 GPTIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRAQFIRSQ 538 GPTIWV IL HEKAIFPYEYPALFS+ +AF+GIWFFS TD S+ +ER L+ QF+RSQ Sbjct: 482 GPTIWVSILHHEKAIFPYEYPALFSMIIAFVGIWFFSITDKSSAAEKERALYFPQFVRSQ 541 Query: 539 TGFGVEQGRAH 549 TG G +H Sbjct: 542 TGLGSSGAVSH 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: 1025 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 17 2021. The underlying query database was built on Sep 17 2021.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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:
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