Align Alpha-ketoglutarate permease of the major facilitator superfamily protein (characterized, see rationale)
to candidate PfGW456L13_4587 dicarboxylic acid transporter PcaT
Query= uniprot:D8J257 (457 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4587 Length = 434 Score = 593 bits (1529), Expect = e-174 Identities = 294/424 (69%), Positives = 352/424 (83%), Gaps = 1/424 (0%) Query: 1 MSDTTQASTPLSAAEYRKRIFAILGASSGNLVEWFDFYVYSFCAIYFAPAFFPKGDPTSQ 60 M+ T + E KRIFAI+GASSGNLVEWFDFYVY+FCAIYFAPAFFP +PT Q Sbjct: 1 MTTPTAPIALYTGEERSKRIFAIVGASSGNLVEWFDFYVYAFCAIYFAPAFFPSDNPTVQ 60 Query: 61 LLNTAGVFAAGFLMRPIGGWLFGRIADKHGRKTSMLISVLMMCGGSLAVAVMPTYATIGA 120 L+NTAGVFAAGFL+RPIGGW+FGR+ADKHGRK SMLIS+LMMC GSL +A +PTY++IG Sbjct: 61 LVNTAGVFAAGFLIRPIGGWIFGRLADKHGRKNSMLISILMMCFGSLLIACLPTYSSIGV 120 Query: 121 WAPALLLLARLFQGLSVGGEYGTSATYMSEVAPNGRRGFFASFQYVTLIGGQLLAVLVLF 180 WAP LLL ARL QGLSVGGEYGT+ATYMSEVA G+RGFFASFQYVTLIGGQLLAV ++ Sbjct: 121 WAPILLLFARLLQGLSVGGEYGTTATYMSEVALKGQRGFFASFQYVTLIGGQLLAVSLVV 180 Query: 181 GMQQWLTKAELMAWGWRVPFVLGAVGALVAMYLRSSLAETSSAGARKKKDAGTLKGLLQ- 239 +QQ+LT+ +L A+GWR+PFV+GA+ ALV++YLR SL ET+S R+ KDAG++ L + Sbjct: 181 VLQQFLTEDDLRAYGWRIPFVVGAMAALVSLYLRRSLKETTSKAMRENKDAGSISALFRD 240 Query: 240 HKRAFLNVVGFTAGGSLMFYTFTTYMQKYLVNTAGMDPKVANGVMTGALFVYMILQPIFG 299 HK AF+ V+G+TAGGSL+FYTFTTYMQKYLVNTAGM K A+ +MTGALF+YM +QPIFG Sbjct: 241 HKTAFITVLGYTAGGSLIFYTFTTYMQKYLVNTAGMPAKTASYIMTGALFLYMCMQPIFG 300 Query: 300 AISDKIGRRNSMLCFAFFGMVGTFPILHFLKDVSSPGVAMALAILALTIVSFYTSISGLI 359 ++DKIGRRNSML F G + T PIL LK V+SP +A L LAL IVSFYTSISGL+ Sbjct: 301 MLADKIGRRNSMLWFGALGTLCTVPILLSLKSVTSPFLAFVLITLALAIVSFYTSISGLV 360 Query: 360 KAEMFPPEVRALGVGLSYAVGNAIFGGSAEFVALSLKSAGIESAFYWYVSALCLVALIIS 419 KAEMFPPEVRALGVGL+YAV NAIFGGSAE+VALSLK+ G+E++FYWYV+ + +A + S Sbjct: 361 KAEMFPPEVRALGVGLAYAVANAIFGGSAEYVALSLKAVGMENSFYWYVTVMMAIAFLFS 420 Query: 420 LRMP 423 LR+P Sbjct: 421 LRLP 424 Lambda K H 0.325 0.138 0.418 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: 731 Number of extensions: 31 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: 457 Length of database: 434 Length adjustment: 32 Effective length of query: 425 Effective length of database: 402 Effective search space: 170850 Effective search space used: 170850 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