Align Acetate permease; SubName: Full=Actetate permease; SubName: Full=Cation acetate symporter; SubName: Full=Cation/acetate symporter (characterized, see rationale)
to candidate PfGW456L13_2421 Acetate permease ActP (cation/acetate symporter)
Query= uniprot:A0A1N7U9G2 (552 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2421 Length = 548 Score = 730 bits (1885), Expect = 0.0 Identities = 367/552 (66%), Positives = 445/552 (80%), Gaps = 5/552 (0%) Query: 2 IRRLLAILGASIFAPAVWAAD-ALTGEVHKQPLNVSAIVMFVVFVGATLCITYWASKRNK 60 + RLLA+ P D A+ + +PLN +AI MF+VFV TL +T WA+ R + Sbjct: 1 MNRLLALF----LLPLAAVTDVAMAADGASRPLNWNAIGMFLVFVLFTLGVTRWAALRTR 56 Query: 61 SAADYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVYTSGYDGLIYSIGFLVGWPIIL 120 S +D+Y AGG +TGFQNGLAIAGD +SAASFLGISA+++ +GYDGL+Y++G L GWPIIL Sbjct: 57 STSDFYTAGGGMTGFQNGLAIAGDMISAASFLGISAMMFLNGYDGLLYALGVLAGWPIIL 116 Query: 121 FLIAERLRNLGKYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFG 180 FLIAERLRNLGKYTFADV SYRL QT +R SA G+L V YL+AQMVGAGKLI+LLFG Sbjct: 117 FLIAERLRNLGKYTFADVVSYRLEQTPVRLTSAFGTLTVALMYLVAQMVGAGKLIELLFG 176 Query: 181 LDYHVAVILVGILMVLYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALF 240 +DY AV+LVG+LMV YV FGGMLATTWVQIIKAV+LL G SFMA MV+KH F A+F Sbjct: 177 IDYLYAVMLVGVLMVFYVTFGGMLATTWVQIIKAVMLLFGTSFMAFMVLKHFGFSTEAMF 236 Query: 241 SEAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSV 300 + A VH KG AIM+PGGL+ +PI A SLGL +MFGTAGLPHILMRFFTVSDAKEARKSV Sbjct: 237 AGATAVHAKGNAIMAPGGLLSNPIDAISLGLGMMFGTAGLPHILMRFFTVSDAKEARKSV 296 Query: 301 FYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALMGGNNMAAVHLANAVGGSIFLG 360 FYATGFIGYFY+L I+GFGAI++V T+PAF+DA+GA++GG NM AVHLA+AVGG++FLG Sbjct: 297 FYATGFIGYFYLLLIIVGFGAIVMVGTDPAFRDASGAIIGGGNMVAVHLAHAVGGNLFLG 356 Query: 361 FISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANDKDEIRVSKITTIALGVLAI 420 FISAVAFATILAVVAGL L+GASAVSHDLYA V++KG+A+++ E+RVS+I T+ +GVLAI Sbjct: 357 FISAVAFATILAVVAGLALSGASAVSHDLYACVMRKGQASEQQEMRVSRIATLCIGVLAI 416 Query: 421 GLGILFESQNIAFMVGLAFSIAASCNFPVLLLSMYWKNLTTRGAMIGGWLGLVSAVGLMV 480 LG+LFESQNIAF+ GL +IAAS NFPVL LSMYWK LTTRGA++G GLVSA+ L+V Sbjct: 417 VLGLLFESQNIAFLSGLVLAIAASVNFPVLFLSMYWKGLTTRGAVLGSLSGLVSAIVLLV 476 Query: 481 LGPTIWVSILHHEKAIFPYEYPALFSMIIAFVGIWFFSITDKSSAAEKERALYFPQFVRS 540 L P +WV+++HH+KA+FPY PALFSM +AF W FS+TD S A ER Y QF+RS Sbjct: 477 LSPAVWVNVMHHDKALFPYSNPALFSMSLAFFSAWLFSVTDTSPRAALERGRYLAQFIRS 536 Query: 541 QTGLGSSGAVSH 552 TG+G++GA H Sbjct: 537 MTGIGATGASKH 548 Lambda K H 0.327 0.140 0.415 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: 1016 Number of extensions: 51 Number of successful extensions: 1 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: 552 Length of database: 548 Length adjustment: 36 Effective length of query: 516 Effective length of database: 512 Effective search space: 264192 Effective search space used: 264192 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 (21.7 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