Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate PfGW456L13_1712 Permeases of the major facilitator superfamily
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1712 Length = 445 Score = 217 bits (552), Expect = 7e-61 Identities = 141/426 (33%), Positives = 212/426 (49%), Gaps = 8/426 (1%) Query: 11 SAAVPAKEKTTASRIKSIFSGSVGNMVEWYDWYVYA-AFSLYFAKAFFPKGDTTAQLLNT 69 S + PA+ +A+R+ + + +G +E+YD+YVYA A +L FFP+ TAQ+L+ Sbjct: 15 SDSTPAQPTNSATRVAT--ASFIGTAIEFYDFYVYATAAALVIGPVFFPQTSGTAQMLSA 72 Query: 70 AAIFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPI 129 F + FL RP+G L G + DR GRK+ L+AS+ LM + +I + PGY++IG API Sbjct: 73 FLTFGIAFLARPLGSALFGHFGDRIGRKSTLVASLLLMGVCTTLIGVLPGYDSIGAWAPI 132 Query: 130 LLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQ 189 LL R QGL +GGE+G +A +E A K +R +F F + G L A G+ + L Sbjct: 133 LLCVLRFGQGLGLGGEWGGAALLATENAPKGKRAWFGMFPQLGPSIGFLAANGLFLTLAV 192 Query: 190 TLTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEETESFAKKEKSKESAMRTLLRHPKEL 249 L EQ WGWRIPF + A +V LY+R + ET FA +E L + Sbjct: 193 VLDDEQFRSWGWRIPFLLSAALVMVGLYVRLKLHETPVFANAMARQERVKIPLFELFGQY 252 Query: 250 MTVVGLTMGGTLA----FYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGG 305 V L G + FY T + Y V T+G S + + P+ Sbjct: 253 WVPVLLGAGAMVVCYALFYISTVFSLSYGVATLGYSRETFLGLLCFAVLFMAAATPLSAW 312 Query: 306 LSDKVGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVK 365 SD+ GR+P+LI G+L L + L TW A FL + ++ + + A++ Sbjct: 313 ASDRYGRKPVLIIGGVLAILSGFLMEPLLTQGSTWGVALFLCIELFLMGVTFAPMGALL- 371 Query: 366 AELFPTEIRALGVGLPYALTVSIFGGTAEYIALWFKSIGMETGYYWYVTACIAVSLLVYV 425 ELFPT +R G Y L + A + A ++G + YV+A +SL+ + Sbjct: 372 PELFPTHVRYTGASAAYNLGGIVGASAAPFFAQKLVAMGGLSYVGGYVSAAAVLSLIAVL 431 Query: 426 TMKDTR 431 +K+TR Sbjct: 432 CLKETR 437 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: 614 Number of extensions: 39 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: 439 Length of database: 445 Length adjustment: 32 Effective length of query: 407 Effective length of database: 413 Effective search space: 168091 Effective search space used: 168091 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