Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate Pf1N1B4_686 Dicarboxylate MFS transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_686 Length = 439 Score = 830 bits (2145), Expect = 0.0 Identities = 414/439 (94%), Positives = 428/439 (97%) Query: 1 MDNSQTLPLGSAAVPAKEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKG 60 MDNS TLPLGSAA+P KEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAK FFP G Sbjct: 1 MDNSNTLPLGSAALPVKEKTTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKTFFPAG 60 Query: 61 DTTAQLLNTAAIFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGY 120 +TAQL+NTAAIFAVGFLMRPIGGWLMGLYADRAGRK ALMASVYLMCFGSL+IALSP Y Sbjct: 61 SSTAQLMNTAAIFAVGFLMRPIGGWLMGLYADRAGRKRALMASVYLMCFGSLLIALSPNY 120 Query: 121 ETIGVGAPILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIA 180 ETIG+GAPILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGF+SSFQYVTLISGQLIA Sbjct: 121 ETIGIGAPILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFYSSFQYVTLISGQLIA 180 Query: 181 LGVLIVLQQTLTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETESFAKKEKSKESAMR 240 L VLIVLQQTLTTEQLY WGWRIPFAIGALCA+VALYLRRGMEETESF KK K+KESAMR Sbjct: 181 LAVLIVLQQTLTTEQLYAWGWRIPFAIGALCAVVALYLRRGMEETESFTKKVKAKESAMR 240 Query: 241 TLLRHPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQ 300 TL+RHPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSI+DST+ISAATLFLFMCLQ Sbjct: 241 TLMRHPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSITDSTSISAATLFLFMCLQ 300 Query: 301 PIIGGLSDKVGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSI 360 PI+GGLSDKVGRRPILIAFGILGTLFTVPILTTLHT+QTWWGAFFLIMAALIIVSGYTSI Sbjct: 301 PIVGGLSDKVGRRPILIAFGILGTLFTVPILTTLHTVQTWWGAFFLIMAALIIVSGYTSI 360 Query: 361 NAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVS 420 NAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVS Sbjct: 361 NAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVS 420 Query: 421 LLVYVTMKDTRKHSRIETD 439 LLVY+TMKDTRKHSRIETD Sbjct: 421 LLVYITMKDTRKHSRIETD 439 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: 858 Number of extensions: 30 Number of successful extensions: 1 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: 439 Length adjustment: 32 Effective length of query: 407 Effective length of database: 407 Effective search space: 165649 Effective search space used: 165649 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