Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate GFF1547 Psest_1584 Arabinose efflux permease
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__psRCH2:GFF1547 Length = 452 Score = 271 bits (694), Expect = 2e-77 Identities = 145/409 (35%), Positives = 227/409 (55%), Gaps = 8/409 (1%) Query: 20 TTASRIKSIFSGSVGNMVEWYDWYVYAAFSLYFAKAFFPKGDTTAQLLNTAAIFAVGFLM 79 T A R + + +GN +EWYD+ V+ ++ ++ FFP + LL A F VGF M Sbjct: 5 TAAPRKNQVLAAVIGNALEWYDFIVFGFLAVVISRLFFPAESEYSALLMATATFGVGFFM 64 Query: 80 RPIGGWLMGLYADRAGRKAALMASVYLMCFGSLIIALSPGYETIGVGAPILLVFARLLQG 139 RPIGG L+G+YADR GRKAAL + LM +IA +P + IG+ AP+L+V ARL+QG Sbjct: 65 RPIGGVLLGIYADRKGRKAALQLIISLMTLSIAMIAFAPPFAAIGIAAPLLIVLARLMQG 124 Query: 140 LSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALGVLIVLQQTLTTEQLYDW 199 + GGE+ ++ ++L E A RRG + S+Q GV ++ L+ E L W Sbjct: 125 FATGGEFASATSFLIESAPANRRGLYGSWQMFGQGLAVFCGAGVTALVTSNLSPEDLDSW 184 Query: 200 GWRIPFAIGALCAIVALYLRRGMEETESFAKKE---KSKESAMRTLLRHPKELMTVVGLT 256 GWRIPF IG + V L++RR + ETE+F + K K+S R L H ++++TV+ LT Sbjct: 185 GWRIPFIIGLIIGPVGLWMRRNLSETEAFLEARQAPKEKQSLARMLRSHLRQVVTVMALT 244 Query: 257 MGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPIL 316 + GT+AFY YM + +GM + D+ T + + L P+ G LSD+VGR+ ++ Sbjct: 245 VCGTVAFYVILVYMPTFANRQLGMQLKDAFTAQVVAVAVLTLLMPVFGALSDRVGRKLLM 304 Query: 317 I--AFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYTSINAVVKAELFPTEIR 374 I G+L L+ P+ + +H ++ + + +++ + + AE FP +R Sbjct: 305 IVATLGLLVALY--PLFSWIHAAPSFGRLLTMQLILCSLLAVFFGPFSAAVAEQFPAGVR 362 Query: 375 ALGVGLPYALTVSIFGGTAEYIALW-FKSIGMETGYYWYVTACIAVSLL 422 + G+ L Y L V IFGG A++I W ++ GM +YV + + L+ Sbjct: 363 STGLALAYNLAVMIFGGFAQFIVTWLIQNTGMAIAPVFYVLFAVTLGLI 411 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: 517 Number of extensions: 29 Number of successful extensions: 5 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: 452 Length adjustment: 32 Effective length of query: 407 Effective length of database: 420 Effective search space: 170940 Effective search space used: 170940 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