Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate WP_083763475.1 AMB_RS08370 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >NCBI__GCF_000009985.1:WP_083763475.1 Length = 445 Score = 578 bits (1491), Expect = e-170 Identities = 285/426 (66%), Positives = 348/426 (81%), Gaps = 3/426 (0%) Query: 17 KEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVG 76 + K T +I +F GSVGN+VE+YDWYVY+AFSLYF+K FFP D T QLLNT+AIFA+G Sbjct: 20 ESKDTKGKILMVFKGSVGNLVEYYDWYVYSAFSLYFSKYFFPGDDPTVQLLNTSAIFALG 79 Query: 77 FLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARL 136 F MRP+GGWL+G +ADR GRKAAL+ SV +MC GSLIIA+ PGY +IGV API L+ ARL Sbjct: 80 FFMRPLGGWLLGTHADRKGRKAALLVSVSMMCAGSLIIAVMPGYNSIGVAAPIALILARL 139 Query: 137 LQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQT-LTTEQ 195 LQGLS+GGEYG++ATYLSE+ATK+RRGF+SSFQYVTLI GQL+ALGVL+ LQ+ LTT + Sbjct: 140 LQGLSLGGEYGSAATYLSEIATKDRRGFYSSFQYVTLIMGQLLALGVLMALQRVFLTTAE 199 Query: 196 LYDWGWRIPFAIGALCAIVALYLRRGMEETESFA--KKEKSKESAMRTLLRHPKELMTVV 253 L WGWRIPF IG LCAIVA+YLR MEETESF K ++ ES +R L+RHP+E++TV+ Sbjct: 200 LEAWGWRIPFVIGGLCAIVAIYLRSSMEETESFEHHKGDRVGESRIRALMRHPREVLTVI 259 Query: 254 GLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRR 313 GLTMGGT+AFYT+TTYMQKYLVNT G S SD+T ISAA F++M + P++G +SDKVGRR Sbjct: 260 GLTMGGTVAFYTFTTYMQKYLVNTAGFSKSDATMISAAATFVYMLMHPLVGHISDKVGRR 319 Query: 314 PILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEI 373 +LIAFG++ TL TVPILT L AFFL+++ L IVSGY++INAVVKAELFP +I Sbjct: 320 AVLIAFGVMSTLCTVPILTALGQTHDSVTAFFLVLSGLTIVSGYSAINAVVKAELFPVQI 379 Query: 374 RALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYVTMKDTRKH 433 RALGVGLP+A+ VS+FGGTAEYIALWFKS+G ET +YWYVT C LL++V MKDT+K Sbjct: 380 RALGVGLPFAIGVSLFGGTAEYIALWFKSMGNETWFYWYVTGCCLCGLLLFVGMKDTKKT 439 Query: 434 SRIETD 439 S I+ D Sbjct: 440 SLIDQD 445 Lambda K H 0.325 0.138 0.414 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: 692 Number of extensions: 34 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: 439 Length of database: 445 Length adjustment: 32 Effective length of query: 407 Effective length of database: 413 Effective search space: 168091 Effective search space used: 168091 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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