Align Cation/acetate symporter ActP; Acetate permease; Acetate transporter ActP (characterized)
to candidate AZOBR_RS02940 AZOBR_RS02940 actetate permease
Query= SwissProt::P32705 (549 letters) >FitnessBrowser__azobra:AZOBR_RS02940 Length = 572 Score = 754 bits (1946), Expect = 0.0 Identities = 378/561 (67%), Positives = 463/561 (82%), Gaps = 20/561 (3%) Query: 7 ALAATLPFAANAADAISGAVERQPTNWQAIIMFLIFVVFTLGITYWASKRVRSRSDYYTA 66 A A +P + +AA A+ GAV++Q TN+ AI+MFL+FV+ TLGITYWA++R +S D+Y A Sbjct: 14 AAGALIPASVHAA-AVEGAVQKQATNFSAIVMFLVFVLATLGITYWAARRTKSAKDFYAA 72 Query: 67 GGNITGFQNGLAIAGDYMSAASFLGISALVFTSGYDGLIYSLGFLVGWPIILFLIAERLR 126 GG ITGFQNGLAIAGDYMSAASFLGI+ LV+TSG+DGLI+S+G+LVGWPIILFL+AERLR Sbjct: 73 GGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGWPIILFLVAERLR 132 Query: 127 NLGRYTFADVASYRLKQGPIRILSACGSLVVVALYLIAQMVGAGKLIELLFGLNYHIAVV 186 NLG+YTFADVASYR +Q P+R ++ACGSL V YLIAQMVGAGKLI+LLFG++Y AVV Sbjct: 133 NLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQLLFGMDYLWAVV 192 Query: 187 LVGVLMMMYVLFGGMLATTWVQIIKAVLLLFGASFMAFMVMKHVGFSFNNLFSEAMAVHP 246 +VGVLM+ YV FGGMLATTWVQIIKAVLLL GASFMAF V+ GFS +FS A+ VHP Sbjct: 193 IVGVLMIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSPEAMFSTAVQVHP 252 Query: 247 KGVDIMKPGGLVKDPISALSLGLGLMFGTAGLPHILMRFFTVSDAREARKSVFYATGFMG 306 K IM PG L+ DP+SA+SLG+ LMFGTAGLPHILMRFFTVSDA+EARKSVFYATGF+G Sbjct: 253 KATGIMAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIG 312 Query: 307 YFYILTFIIGFGAIMLV------GANPEYKDAA-----------GHLIGGNNMAAVHLAN 349 YFYILTFIIGFGAI+L+ GA P + DAA +IGG+NMAA+H A+ Sbjct: 313 YFYILTFIIGFGAIVLLLAPDATGAYP-FLDAAKLAAAGGKPNPSMIIGGSNMAAIHTAH 371 Query: 350 AVGGNLFLGFISAVAFATILAVVAGLTLAGASAVSHDLYANVFKKG-ATEREELRVSKIT 408 AVGG+LF GFISAVAFATILAVVAGLTLAGASAVSHDLYA+V KG A+E +E+RVSKIT Sbjct: 372 AVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRASEHDEIRVSKIT 431 Query: 409 VLILGVIAIILGVLFENQNIAFMVGLAFAIAASCNFPIILLSMYWSKLTTRGAMMGGWLG 468 +I+G+++I LG+ FENQN+AFMVGLAF IAAS NFP++L+SM+WS++TTRGA++GGW+G Sbjct: 432 TVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMTTRGAVLGGWIG 491 Query: 469 LITAVVLMILGPTIWVQILGHEKAIFPYEYPALFSITVAFLGIWFFSATDNSAEGARERE 528 L+++V L+I+GPT+W +LG+ A+FPY+ P +F+I ++FL IWFFS TDNS ERE Sbjct: 492 LVSSVSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSITDNSKAAQDERE 551 Query: 529 LFRAQFIRSQTGFGVEQGRAH 549 ++AQ+IRSQTG G E AH Sbjct: 552 AYKAQYIRSQTGLGAEGASAH 572 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: 1027 Number of extensions: 43 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: 572 Length adjustment: 36 Effective length of query: 513 Effective length of database: 536 Effective search space: 274968 Effective search space used: 274968 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