Align Acetate transporter (characterized, see rationale)
to candidate AZOBR_RS02940 AZOBR_RS02940 actetate permease
Query= uniprot:G8AHY6 (572 letters) >FitnessBrowser__azobra:AZOBR_RS02940 Length = 572 Score = 1107 bits (2862), Expect = 0.0 Identities = 572/572 (100%), Positives = 572/572 (100%) Query: 1 MRSLVNRVGVAAVAAGALIPASVHAAAVEGAVQKQATNFSAIVMFLVFVLATLGITYWAA 60 MRSLVNRVGVAAVAAGALIPASVHAAAVEGAVQKQATNFSAIVMFLVFVLATLGITYWAA Sbjct: 1 MRSLVNRVGVAAVAAGALIPASVHAAAVEGAVQKQATNFSAIVMFLVFVLATLGITYWAA 60 Query: 61 RRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGW 120 RRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGW Sbjct: 61 RRTKSAKDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGW 120 Query: 121 PIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQ 180 PIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQ Sbjct: 121 PIILFLVAERLRNLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQ 180 Query: 181 LLFGMDYLWAVVIVGVLMIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSP 240 LLFGMDYLWAVVIVGVLMIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSP Sbjct: 181 LLFGMDYLWAVVIVGVLMIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSP 240 Query: 241 EAMFSTAVQVHPKATGIMAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEA 300 EAMFSTAVQVHPKATGIMAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEA Sbjct: 241 EAMFSTAVQVHPKATGIMAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEA 300 Query: 301 RKSVFYATGFIGYFYILTFIIGFGAIVLLLAPDATGAYPFLDAAKLAAAGGKPNPSMIIG 360 RKSVFYATGFIGYFYILTFIIGFGAIVLLLAPDATGAYPFLDAAKLAAAGGKPNPSMIIG Sbjct: 301 RKSVFYATGFIGYFYILTFIIGFGAIVLLLAPDATGAYPFLDAAKLAAAGGKPNPSMIIG 360 Query: 361 GSNMAAIHTAHAVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRAS 420 GSNMAAIHTAHAVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRAS Sbjct: 361 GSNMAAIHTAHAVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRAS 420 Query: 421 EHDEIRVSKITTVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMT 480 EHDEIRVSKITTVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMT Sbjct: 421 EHDEIRVSKITTVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMT 480 Query: 481 TRGAVLGGWIGLVSSVSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSIT 540 TRGAVLGGWIGLVSSVSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSIT Sbjct: 481 TRGAVLGGWIGLVSSVSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSIT 540 Query: 541 DNSKAAQDEREAYKAQYIRSQTGLGAEGASAH 572 DNSKAAQDEREAYKAQYIRSQTGLGAEGASAH Sbjct: 541 DNSKAAQDEREAYKAQYIRSQTGLGAEGASAH 572 Lambda K H 0.327 0.138 0.410 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: 1344 Number of extensions: 52 Number of successful extensions: 3 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: 572 Length of database: 572 Length adjustment: 36 Effective length of query: 536 Effective length of database: 536 Effective search space: 287296 Effective search space used: 287296 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