Align Acetate transporter (characterized, see rationale)
to candidate WP_011386681.1 AMB_RS21920 cation acetate symporter
Query= uniprot:G8AHY6 (572 letters) >NCBI__GCF_000009985.1:WP_011386681.1 Length = 554 Score = 697 bits (1800), Expect = 0.0 Identities = 357/566 (63%), Positives = 440/566 (77%), Gaps = 17/566 (3%) Query: 7 RVGVAAVAAGALIPASVHAAAVEGAVQKQATNFSAIVMFLVFVLATLGITYWAARRTKSA 66 R+GV ++ A ++ A A G +QATN+ AI+MF+ FVL TLGIT+WA++RTKSA Sbjct: 6 RLGVLSLMLLAPSLPALAAGADLGQAARQATNWHAILMFVGFVLLTLGITWWASKRTKSA 65 Query: 67 KDFYAAGGGITGFQNGLAIAGDYMSAASFLGIAGLVYTSGFDGLIFSVGWLVGWPIILFL 126 DFY AGGGITGFQNGLAIAGD+MSAASFLG+ L+Y +G DG++++VG +VGWP++LFL Sbjct: 66 ADFYTAGGGITGFQNGLAIAGDFMSAASFLGVTALLYGTGLDGMVYAVGVVVGWPLMLFL 125 Query: 127 VAERLRNLGKYTFADVASYRFQQTPMRTMAACGSLATVTFYLIAQMVGAGKLIQLLFGMD 186 +AE LRNLGKYTFADV +YR + P+RT AA SL V FYLIAQMVGAG+LI+LLFGMD Sbjct: 126 IAEPLRNLGKYTFADVVAYRLAKVPVRTYAAFSSLTVVVFYLIAQMVGAGQLIKLLFGMD 185 Query: 187 YLWAVVIVGVLMIAYVTFGGMLATTWVQIIKAVLLLSGASFMAFAVLAKFGFSPEAMFST 246 YL+A+ +VG LM+ YVTFGGM ATTWVQIIKAVLLLSGA+FMA AVL++FGFSPEAMF+ Sbjct: 186 YLYALFLVGGLMMIYVTFGGMAATTWVQIIKAVLLLSGATFMAGAVLSRFGFSPEAMFAK 245 Query: 247 AVQVHPKATGIMAPGALITDPVSAISLGMALMFGTAGLPHILMRFFTVSDAKEARKSVFY 306 AVQV + IM+PG L DP+ ISL MAL FGTAGLPHILMRFFTV DAKEARKSVFY Sbjct: 246 AVQV-KGSNAIMSPGLLFKDPIDTISLAMALAFGTAGLPHILMRFFTVPDAKEARKSVFY 304 Query: 307 ATGFIGYFYILTFIIGFGAIVLLLAPDATGAYPFLDAAKLAAAGGKPNPSMIIGGSNMAA 366 AT FIG+FY+L +IG GAI L+A D T A GK + GG NMAA Sbjct: 305 ATAFIGFFYVLAVVIGIGAIA-LVATDPT-----------YLADGK----ALKGGGNMAA 348 Query: 367 IHTAHAVGGDLFFGFISAVAFATILAVVAGLTLAGASAVSHDLYASVIAKGRASEHDEIR 426 + AHAVGGDLF GFISAVAFATILAVVAGLTLAGASA+SHDLYA+V A+G A E E+R Sbjct: 349 VWLAHAVGGDLFLGFISAVAFATILAVVAGLTLAGASAISHDLYANVFARGHAKEETELR 408 Query: 427 VSKITTVIIGIVSIFLGIAFENQNVAFMVGLAFVIAASANFPVLLMSMFWSRMTTRGAVL 486 +S++ ++ +G+++I LG+ FE QN+A++ GL IAASANFP+LL+SM W +T+RGA+L Sbjct: 409 ISRLASLALGVIAIILGMLFEKQNIAYLAGLTLAIAASANFPLLLLSMLWPGLTSRGAIL 468 Query: 487 GGWIGLVSSVSLLIMGPTVWKSVLGNPAALFPYDNPGVFTIPLSFLAIWFFSITDNSKAA 546 GG GLVS+V L ++GP VWK+VLGNP +FP+ NP +F++ F A WFFS+TD S+ A Sbjct: 469 GGVAGLVSAVVLTVLGPAVWKAVLGNPQPIFPWGNPALFSVAAGFAATWFFSVTDGSERA 528 Query: 547 QDEREAYKAQYIRSQTGLGAEGASAH 572 E+ + AQ++RSQTGLGAEG SAH Sbjct: 529 VREKAEFNAQFVRSQTGLGAEGVSAH 554 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: 1102 Number of extensions: 61 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: 572 Length of database: 554 Length adjustment: 36 Effective length of query: 536 Effective length of database: 518 Effective search space: 277648 Effective search space used: 277648 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