Align Alpha-ketoglutarate permease, MFS superfamily (characterized)
to candidate BPHYT_RS07505 BPHYT_RS07505 major facilitator transporter
Query= reanno::pseudo3_N2E3:AO353_03810 (439 letters) >FitnessBrowser__BFirm:BPHYT_RS07505 Length = 453 Score = 260 bits (665), Expect = 5e-74 Identities = 157/452 (34%), Positives = 244/452 (53%), Gaps = 27/452 (5%) Query: 1 MDNSQT-LPLGSAAVPAKEKTTA------SRIKSIFSGSVGNMVEWYDWYVYAAFSLYFA 53 MD S T P G+ A+ + A S +K+I + ++GN +E++D+ +Y+ F+ Sbjct: 1 MDYSATPQPAGTEALSMQSTPAAQPVERTSHVKAIAAITLGNGLEFFDFTIYSFFATIIG 60 Query: 54 KAFFPKGDTTAQLLNTAAIFAVGFLMRPIGGWLMGLYADRAGRKAALMASVYLMCFGSLI 113 K +FP AQL+ F VGF+MRP+GG ++G YADRAGRKAA+ +++LM GS I Sbjct: 61 KLYFPVEGQLAQLMLAVGTFGVGFIMRPVGGIVLGAYADRAGRKAAMSLTLWLMTLGSAI 120 Query: 114 IALSPGYETIGVGAPILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVT- 172 IA +P Y IGV AP+L++ ARL+QG ++GGE G S + L E + + RGF+ S+Q+V+ Sbjct: 121 IAFAPTYAAIGVAAPLLVILARLIQGFALGGEVGASTSLLLEYGSNKTRGFYGSWQFVSQ 180 Query: 173 ---LISGQLIALGVLIVLQQTLTTEQLYDWGWRIPFAIGALCAIVALYLRRGMEET---- 225 + G L+ + L L+T L WGWR+PF IG + +Y+RR + ET Sbjct: 181 GLNTVCGSLLG----VALAAALSTAALESWGWRVPFVIGMAMGPIGIYIRRHLNETLPGV 236 Query: 226 -ESFAKKEKSKE---SAMRTLLR-HPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGM 280 + A + + +R L R H + + T V T+GGT A Y Y+ Y + + + Sbjct: 237 EDGAAGSQPGSQPVSQPVRKLFREHSRVITTGVLTTIGGTAANYIVLFYLSTYAIRILHL 296 Query: 281 SISDSTTISAATLFLFMCLQPIIGGLSDKVGRRPILIAFGILGTLFTVPILTTLHTIQTW 340 +S + + + + P G LSD+VGR+ +L +L P ++ T Sbjct: 297 PMSSALWAAWTAAVVTVICSPFAGALSDRVGRKRVLWVSRVLLIAAVYPAFMMINASPT- 355 Query: 341 WGAFFLIMAALIIVSGYTSI-NAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYIALW 399 ++A L ++ +T++ N V+ E+FP EIRA G+ + Y L VSIFGG A++ A W Sbjct: 356 VPVLLAVVAGLAVLVAFTAVPNIVMLPEMFPREIRATGMSIVYCLGVSIFGGFAQFFATW 415 Query: 400 FKSI-GMETGYYWYVTACIAVSLLVYVTMKDT 430 + G WY+ C VSLL M++T Sbjct: 416 LIQVSGSNLAPAWYLIGCGVVSLLPLPFMRET 447 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: 569 Number of extensions: 31 Number of successful extensions: 6 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: 453 Length adjustment: 32 Effective length of query: 407 Effective length of database: 421 Effective search space: 171347 Effective search space used: 171347 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