Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate Pf6N2E2_1184 L-Proline/Glycine betaine transporter ProP
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1184 Length = 434 Score = 229 bits (583), Expect = 2e-64 Identities = 145/416 (34%), Positives = 217/416 (52%), Gaps = 10/416 (2%) Query: 24 RIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLMRPIG 83 R K + + SVG +EW+D+ ++A FSL A AFFP D LL + AVGF+ RP+G Sbjct: 8 RRKLVLAVSVGAALEWFDFTLFAIFSLQIAAAFFPASDPLMSLLASYLALAVGFVARPLG 67 Query: 84 GWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQGLSVG 143 LMG YADR GRKAAL S+ LM G+LIIA+ P YETIG AP+ +V AR+LQG++ G Sbjct: 68 ALLMGRYADRQGRKAALTLSIMLMGAGTLIIAVCPTYETIGWWAPLSVVVARILQGVAAG 127 Query: 144 GEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDWGWRI 203 GE G + YL E A +RR F+S Q V L+ +L LT QL +WGWR+ Sbjct: 128 GEIGGALAYLVETAPADRRALFASSQQVAQAGSFLLCGLSASLLSSALTPAQLDEWGWRV 187 Query: 204 PFAIGALCAIVALYLRRGMEETESFAK-KEKSKESAMRTLLRHPKELMTVVGLTMGGTL- 261 P+ G L + L +RR +EE+E + + + AM + P + L MG + Sbjct: 188 PYVFGLLVVVAGLKIRRSLEESEPLRRFLDNQDKHAMAG--KGPSLRPYLPNLVMGVLIV 245 Query: 262 AFYTYTTYMQKYLVNTVGMSIS---DSTTISAATLFLFMCLQPIIGGLSDKVGRRPILIA 318 +T T + ++ M + + + + L L P+ LSD++GR +++ Sbjct: 246 VLWTVATQLINFIPTYASMVLELPRNKAYLGLVLVGLITLLCPLTALLSDRIGRYTVMLI 305 Query: 319 FGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIRALGV 378 + L P L+ + A +++ YT A AELFP ++RALGV Sbjct: 306 GAVGVALCAYPGFVWLNNSPSLQTLIIFQCALAVLMVLYTGPAAAALAELFPVQVRALGV 365 Query: 379 GLPYALTVSIFG-GTAEYIALWFKSIG--METGYYWYVTACIAVSLLVYVTMKDTR 431 L YAL+V++FG T I L ++ G + ++ + AC++ L +V++ R Sbjct: 366 SLAYALSVTLFGSATPALITLIYRQSGDALAAAHWLFAAACLSAIPLAWVSLSKYR 421 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: 490 Number of extensions: 25 Number of successful extensions: 2 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: 434 Length adjustment: 32 Effective length of query: 407 Effective length of database: 402 Effective search space: 163614 Effective search space used: 163614 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