Align Cation acetate symporter (characterized, see rationale)
to candidate BWI76_RS02085 BWI76_RS02085 cation acetate symporter
Query= uniprot:A0A166PH03 (552 letters) >FitnessBrowser__Koxy:BWI76_RS02085 Length = 549 Score = 866 bits (2238), Expect = 0.0 Identities = 444/552 (80%), Positives = 487/552 (88%), Gaps = 3/552 (0%) Query: 1 MIRRLMALLSIAAFAPGVWAAEALTGAVQKQPLNVSAILMFVAFVGATLCITYWASKRNN 60 M + L AL + F AA+A+TGAVQ+QP N AI+MF+ FV TL ITYWASKR Sbjct: 1 MKKVLTALAATLPFTAN--AADAITGAVQRQPTNWQAIIMFLIFVALTLYITYWASKRVR 58 Query: 61 SAADYYAAGGKITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSIGFLVGWPIIL 120 S +DYY AGG ITGFQNGLAIAGD+MSAASFLGISALV+TSGYDGLIYS+GFLVGWPIIL Sbjct: 59 SRSDYYTAGGNITGFQNGLAIAGDFMSAASFLGISALVYTSGYDGLIYSLGFLVGWPIIL 118 Query: 121 FLIAERLRNLGKYTFADVASYRLGQTQIRSLSACGSLVVVAFYLIAQMVGAGKLIQLLFG 180 FLIAERLRNLG+YTFADVASYRL Q IR+LSACGSLVVVA YLIAQMVGAGKLIQLLFG Sbjct: 119 FLIAERLRNLGRYTFADVASYRLKQGPIRTLSACGSLVVVALYLIAQMVGAGKLIQLLFG 178 Query: 181 LDYHVAVILVGILMCMYVLFGGMLATTWVQIIKAVLLLSGASFMALMVMKHVNFDFNALF 240 L+YH+AV+LVG+LM +YVLFGGMLATTWVQIIKAVLLL GASFMA MVMKHV F FN LF Sbjct: 179 LNYHIAVVLVGVLMVLYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLF 238 Query: 241 SEAIKVHPKGEAIMSPGGLVKDPISAFSLGLALMFGTAGLPHILMRFFTVSDAKEARKSV 300 SEA+ VHPKG AIMSPGGLVKDPISA SLGL LMFGTAGLPHILMRFFTVSDAKEARKSV Sbjct: 239 SEAMAVHPKGAAIMSPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAKEARKSV 298 Query: 301 LYATGFIGYFYILTFIIGFGAILLVSTNPAFKDAAGALMGGNNMAAVHLANAVGGSVFLG 360 YATGF+GYFYILTFIIGFGAI+LV NPAFKDAAG L+GGNNMAAVHLA+AVGG++FLG Sbjct: 299 FYATGFMGYFYILTFIIGFGAIMLVGANPAFKDAAGQLIGGNNMAAVHLADAVGGNLFLG 358 Query: 361 FISAVAFATILAVVAGLTLAGASAVSHDLYASVIKKGKANEKDEIRVSKITTIALAVLAI 420 FISAVAFATILAVVAGLTLAGASAVSHDLYA+V +KG A E+ E++VSKIT + L V+AI Sbjct: 359 FISAVAFATILAVVAGLTLAGASAVSHDLYANVFRKG-ATERQELKVSKITVLILGVVAI 417 Query: 421 GLGILFEKQNIAFMVGLAFSIAASCNFPVLLLSMYWKKLTTRGAMVGGWLGLVSAVGLMV 480 LGILFE QNIAFMVGLAFSIAASCNFP++LLSMYW KLTTRGAM+GGWLGL++AV LMV Sbjct: 418 LLGILFENQNIAFMVGLAFSIAASCNFPIILLSMYWSKLTTRGAMIGGWLGLLTAVILMV 477 Query: 481 LGPTIWVQILGHEKAIFPYEYPALFSMAIAFVGIWFFSVTDKSAEGVNERALFFPQFVRS 540 LGPTIWVQILGHEKAIFPYEYPALFS+A+AF+GIWFFS TD SAEG ER LF QF+RS Sbjct: 478 LGPTIWVQILGHEKAIFPYEYPALFSIAVAFIGIWFFSATDNSAEGSRERELFRAQFIRS 537 Query: 541 QTGLGASGAVSH 552 QTG+G +H Sbjct: 538 QTGIGIEKGQAH 549 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: 1075 Number of extensions: 54 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: 552 Length of database: 549 Length adjustment: 36 Effective length of query: 516 Effective length of database: 513 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 (21.7 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