Align Acetate transporter (characterized, see rationale)
to candidate WP_011385106.1 AMB_RS13720 cation acetate symporter
Query= uniprot:G8AHY6 (572 letters) >NCBI__GCF_000009985.1:WP_011385106.1 Length = 561 Score = 734 bits (1894), Expect = 0.0 Identities = 377/557 (67%), Positives = 445/557 (79%), Gaps = 17/557 (3%) Query: 18 LIPASVHAAAVEGAVQKQATNFSAIVMFLVFVLATLGITYWAARRTKSAKDFYAAGGGIT 77 L A++ A A G +KQATN+ AI+MF++FV TLGITYWAA RTK+A DFYAAGGGIT Sbjct: 20 LASAALAAGADMGGAEKQATNWHAIIMFVIFVGMTLGITYWAAGRTKTAADFYAAGGGIT 79 Query: 78 GFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGWPIILFLVAERLRNLGKY 137 GFQNGLAIAGDYMSAASFLGI+ LVY SG+DGLIFSVGWLVGWPIILFL+AERLRNLGKY Sbjct: 80 GFQNGLAIAGDYMSAASFLGISALVYGSGYDGLIFSVGWLVGWPIILFLIAERLRNLGKY 139 Query: 138 TFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQLLFGMDYLWAVVIVGVL 197 TFADV YR +TP+RT AA GSL V FYLI QMVGAG+LI+LLFGMDY++AV+IVG L Sbjct: 140 TFADVCGYRLARTPIRTFAATGSLIVVIFYLIGQMVGAGQLIKLLFGMDYIYAVMIVGAL 199 Query: 198 MIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSPEAMFSTAVQVHPKATGI 257 M+ YVTFGGM+ATTWVQIIKA LLL GA+F+AF V++ FGFS E +F A++VHPK I Sbjct: 200 MMVYVTFGGMVATTWVQIIKACLLLGGATFIAFGVMSHFGFSFEKLFVKAIEVHPKKVAI 259 Query: 258 MAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEARKSVFYATGFIGYFYIL 317 MAPGAL+T+PV AISLGMALMFGTAGLPHILMRFFTV DA+EARKSVFYATGFIGYFYIL Sbjct: 260 MAPGALVTNPVDAISLGMALMFGTAGLPHILMRFFTVPDAREARKSVFYATGFIGYFYIL 319 Query: 318 TFIIGFGAIVLLLA-PD-ATGAYPFLDAAKLAAAGGKPNPSMIIGGSNMAAIHTAHAVGG 375 TFIIGFGAI L+ P+ T LD + GG+NMAA+ AHA+GG Sbjct: 320 TFIIGFGAITLVATNPEYLTKGLGSLD---------------LKGGNNMAAVWLAHAIGG 364 Query: 376 DLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRASEHDEIRVSKITTVII 435 DLF GFISAVAFATILAVV+GLTLAGASA+SHDLYASVI G+A+E E+ VSKI ++ + Sbjct: 365 DLFLGFISAVAFATILAVVSGLTLAGASAISHDLYASVIMHGQATEGREVTVSKIASIGL 424 Query: 436 GIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMTTRGAVLGGWIGLVSS 495 GI+++ LG+ FE QNVAF+V L F +AASANFPVL++SMFW +TTRGAVLGG IGL+ S Sbjct: 425 GIIAVLLGLVFEKQNVAFIVALTFSVAASANFPVLVLSMFWGGLTTRGAVLGGMIGLLMS 484 Query: 496 VSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSITDNSKAAQDEREAYKA 555 V ++++ VW G A +FP+ P +F++P +F W FSI DNS AQ ER AY+A Sbjct: 485 VIMVVLSKAVWVQSFGFKAEIFPFAYPALFSVPAAFFFSWLFSILDNSPQAQAERAAYEA 544 Query: 556 QYIRSQTGLGAEGASAH 572 Q IRS+TGLGAEGA++H Sbjct: 545 QSIRSETGLGAEGAASH 561 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: 1159 Number of extensions: 64 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: 572 Length of database: 561 Length adjustment: 36 Effective length of query: 536 Effective length of database: 525 Effective search space: 281400 Effective search space used: 281400 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