Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate N515DRAFT_0011 N515DRAFT_0011 MFS transporter, MHS family, alpha-ketoglutarate permease
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__Dyella79:N515DRAFT_0011 Length = 435 Score = 619 bits (1597), Expect = 0.0 Identities = 301/425 (70%), Positives = 357/425 (84%), Gaps = 2/425 (0%) Query: 16 AKEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAV 75 A T R++SIFSGS+GN+VEWYDWYVY+AFSLYFA+ FFP D T QLLNT+ IFAV Sbjct: 12 APAMTAGQRLRSIFSGSIGNLVEWYDWYVYSAFSLYFAQVFFPASDQTTQLLNTSGIFAV 71 Query: 76 GFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFAR 135 GFLMRP+GGWL+G +ADR GRKAAL+ SV++M GSLII LSPGY IGV APILLV AR Sbjct: 72 GFLMRPLGGWLLGTFADRRGRKAALLLSVFMMSLGSLIIGLSPGYAQIGVAAPILLVLAR 131 Query: 136 LLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQ-TLTTE 194 LLQGLS+GGEYGTSATYLSEMA +E RGF+SS QYVTL++GQLIAL +L+VLQ L+T+ Sbjct: 132 LLQGLSIGGEYGTSATYLSEMAPRESRGFWSSIQYVTLVAGQLIALALLVVLQHFVLSTQ 191 Query: 195 QLYDWGWRIPFAIGALCAIVALYLRRGMEETESFAKKEKSKESAMRTLLRHPKELMTVVG 254 QL+DWGWRIPF IGAL A++A+ +RR M+ET SF KK + ES +RTL+RHP+E++TV+G Sbjct: 192 QLHDWGWRIPFLIGALLAVIAVIIRRNMDETASF-KKARQLESPLRTLMRHPREVLTVIG 250 Query: 255 LTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRP 314 LTMGGTLAFYT+TTYMQK+LVN+ GMS +D+T+IS A LF++ LQP G LSD++GRRP Sbjct: 251 LTMGGTLAFYTFTTYMQKFLVNSAGMSKADATSISTAALFVYALLQPAFGALSDRIGRRP 310 Query: 315 ILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIR 374 +LI FG+LG L T PIL+TL WW AF LIMAALIIVSGYTSINAVVKAELFPTEIR Sbjct: 311 LLIGFGVLGALLTYPILSTLKEAHDWWQAFGLIMAALIIVSGYTSINAVVKAELFPTEIR 370 Query: 375 ALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYVTMKDTRKHS 434 A+GVGLPYAL +S+FGGTAEY+ALWFK IG E +YWYVTACIA SLLVY+ M+DTR+HS Sbjct: 371 AIGVGLPYALALSVFGGTAEYVALWFKKIGHEDYFYWYVTACIACSLLVYIGMRDTRRHS 430 Query: 435 RIETD 439 RI D Sbjct: 431 RIVED 435 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: 715 Number of extensions: 33 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: 439 Length of database: 435 Length adjustment: 32 Effective length of query: 407 Effective length of database: 403 Effective search space: 164021 Effective search space used: 164021 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