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.
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