Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate BWI76_RS08245 BWI76_RS08245 MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__Koxy:BWI76_RS08245 Length = 431 Score = 231 bits (589), Expect = 3e-65 Identities = 134/386 (34%), Positives = 209/386 (54%), Gaps = 18/386 (4%) Query: 22 ASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRP 81 A I +I + GN +E +D++++ ++ Y A+ FFP A L+ T A+F GFLMRP Sbjct: 8 AGTIGAILRVTSGNFLEQFDFFLFGFYATYIARTFFPAESEFAALMLTFAVFGSGFLMRP 67 Query: 82 IGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLS 141 IG ++G Y DR GR+ LM ++ +M G+L+IAL PGY+TIG+ APIL+V RLLQG S Sbjct: 68 IGAIVLGAYIDRIGRRKGLMVTLAIMGCGTLLIALVPGYQTIGILAPILVVVGRLLQGFS 127 Query: 142 VGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGW 201 G E G + YLSE+AT +GF++S+Q + ++A + L +TL +Q+ +WGW Sbjct: 128 AGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYALNETLGHDQIAEWGW 187 Query: 202 RIPFAIGALCAIVALYLRRGMEETESFAKKEKSKES--AMRTLLRHPKELMTVVGLTMGG 259 RIPF IG + + LRR ++ETE+F +++ ++ + T++++ + + L Sbjct: 188 RIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTREILSTIVKNWRIISAGTLLVAMT 247 Query: 260 TLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPILIAF 319 T FY T Y Y + +S DS ++ PI G +SDK+GRRP+L+ Sbjct: 248 TTTFYFITVYTPTYGRAVLHLSARDSLLVTMLVGISNFIWLPIGGAISDKIGRRPVLMGI 307 Query: 320 GILGTLFTVPIL--------TTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPT 371 +L L T P++ T T+ W +FF M Y E+ P Sbjct: 308 TLLALLTTWPVMHWLTAAPDFTRMTLVLLWFSFFFGM--------YNGAMVAALTEVMPV 359 Query: 372 EIRALGVGLPYALTVSIFGGTAEYIA 397 +R +G L ++L +IFGG I+ Sbjct: 360 YVRTVGFSLAFSLATAIFGGLTPAIS 385 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: 558 Number of extensions: 30 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: 431 Length adjustment: 32 Effective length of query: 407 Effective length of database: 399 Effective search space: 162393 Effective search space used: 162393 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