Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate WP_013460689.1 SULKU_RS09190 cation acetate symporter
Query= SwissProt::P32705 (549 letters) >NCBI__GCF_000183725.1:WP_013460689.1 Length = 552 Score = 760 bits (1963), Expect = 0.0 Identities = 388/557 (69%), Positives = 463/557 (83%), Gaps = 13/557 (2%) Query: 1 MKRVLTALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSR 60 MK + AL + AA A +A+SGAVE+QP N AIIMFLIFV TLGITYWA+KR ++ Sbjct: 1 MKALFLALFSV---AAFAGEALSGAVEKQPLNMSAIIMFLIFVGATLGITYWAAKRTKTA 57 Query: 61 SDYYTAGGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFL 120 D+YTAGG ITGFQNG+AIAGDYMSAASFLGISALV+ GYDGLIYS+GFLVGWPIILF+ Sbjct: 58 KDFYTAGGGITGFQNGMAIAGDYMSAASFLGISALVYAKGYDGLIYSIGFLVGWPIILFM 117 Query: 121 IAERLRNLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLN 180 +AE+LRNLG+YTFADVASYRL+Q PIR L+A GS++ V LYLIAQMVGAGKLI+LLFGL+ Sbjct: 118 VAEQLRNLGKYTFADVASYRLRQTPIRTLAAFGSILTVVLYLIAQMVGAGKLIQLLFGLD 177 Query: 181 YHIAVVLVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSE 240 Y IAV+LVGVLM++YV FGGMLATTWVQIIKA LLL GA+FMA VM H F+F +LF Sbjct: 178 YEIAVILVGVLMILYVTFGGMLATTWVQIIKAFLLLSGATFMAVAVMAHYNFNFESLF-- 235 Query: 241 AMAVHPKGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFY 300 A AV K IM PG LV DPISA+SLG+ LMFGTAGLPHILMRFFTVSDA+EARKSVFY Sbjct: 236 ATAVSMKDQSIMAPGKLVSDPISAISLGIALMFGTAGLPHILMRFFTVSDAKEARKSVFY 295 Query: 301 ATGFMGYFYILTFIIGFGAIMLVGANPEYKDAA-------GHLIGGNNMAAVHLANAVGG 353 ATGF+GYFYILTFIIGFGAI++V NP+Y D A ++GG+NMAA+HL++AVGG Sbjct: 296 ATGFIGYFYILTFIIGFGAIVMVFQNPQYLDLAKQAVDGGAPILGGDNMAAIHLSHAVGG 355 Query: 354 NLFLGFISAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKITVLIL 412 + FLGF+SAVAFATILAVV+GLTLAGASA+SHDLYA+V + G A E++VSKI+ ++L Sbjct: 356 DFFLGFMSAVAFATILAVVSGLTLAGASAISHDLYASVLRAGRADGMMEMKVSKISTVVL 415 Query: 413 GVIAIILGVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLGLITA 472 G++AI LG+ FE+QNIAFMVGLAFAIAAS NFPI+ LSM+WSKLTTRGA++GG LGL+TA Sbjct: 416 GIVAIYLGIAFEDQNIAFMVGLAFAIAASANFPILFLSMFWSKLTTRGALLGGSLGLLTA 475 Query: 473 VVLMILGPTIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERELFRA 532 VL++LGPT+WV +L + +AIFPY+YPALFS++ AF+GIWFFS TD S +E+E + A Sbjct: 476 GVLVVLGPTVWVDVLKNAEAIFPYKYPALFSVSAAFIGIWFFSITDKSENSEKEKEAYEA 535 Query: 533 QFIRSQTGFGVEQGRAH 549 Q+IRSQTG G E H Sbjct: 536 QYIRSQTGIGAEGAVEH 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: 1015 Number of extensions: 47 Number of successful extensions: 4 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 24 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