Align MFS transporter (characterized, see rationale)
to candidate BPHYT_RS31135 BPHYT_RS31135 hexuranate MFS transporter
Query= uniprot:A0A166QG26 (467 letters) >FitnessBrowser__BFirm:BPHYT_RS31135 Length = 429 Score = 376 bits (965), Expect = e-109 Identities = 195/448 (43%), Positives = 264/448 (58%), Gaps = 42/448 (9%) Query: 15 AVGNYRWTICALLFFATTVNYLDRQVLSLLAPDLSTQFGWSNSDYANIASVFQFVYAISM 74 AVG YRWTICAL+FFATT+NY+DRQ+L LLAP L GW+ YA VF YA+ + Sbjct: 14 AVGRYRWTICALIFFATTINYMDRQMLGLLAPLLQKDIGWTQVQYAQTVMVFTVAYAVGL 73 Query: 75 LFAGRVVDKIGTKTAYVVAICIWSTGAVMHAFAVPMGEGIGAVSSALGIAMIPVSIAGFM 134 GR+ D+I TK Y A+ +WS A++HA A ++ GF Sbjct: 74 ATFGRIADRISTKVVYGGAMAMWSLAAMLHAIAA--------------------TVPGFA 113 Query: 135 VSRAVLAIGEAGNFPIAIKATAEYFPKKERSFATGIFNSGANVGAILAPICVPLIASLWG 194 R +L GEA NFP+AI+ TA +FPKKER+ ATG++N GA VG I+AP VP+ A +WG Sbjct: 114 AVRGLLGFGEAANFPVAIRTTALWFPKKERALATGLWNMGATVGGIVAPAFVPIAAVMWG 173 Query: 195 WEAAFIVIGMLGFVWVGVWIALYEKPEQQKRLSAQELAYIRSDQVVPVVTRPVPGVADKK 254 W A FI G GFVW+ VW+ +Y P + +S +EL YI SD+ V +++ Sbjct: 174 WRATFIAGGAAGFVWLAVWLLVYRPPAEHASVSKRELDYINSDRDESV---------EQR 224 Query: 255 VSWFKLLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQYGMKGQAIVMPLAVLYSMTM 314 VSW +L YR+TWAF FGK +TD VWWF+LFWLP +L+ + + +PL V+Y+M Sbjct: 225 VSWLSVLKYRETWAFIFGKLLTDPVWWFYLFWLPKWLNESRHIDIANLGLPLIVIYTMAS 284 Query: 315 IGSIGGGWFPSYFMSRGDAPYDGRMKAMLVIAFFPLLVLLAQPLG-YISFWVPVLLIGVG 373 +GS+ GGW S M R P R AM V A L VL L + S W V +G+ Sbjct: 285 VGSVAGGWLSSRLMQRSHKPNVARKIAMGVCA---LCVLPIATLSLFQSLWYAVFAVGLA 341 Query: 374 ASAHQAWSCNIFTTVSDMFPQKSIASVVGIGGLAGGLGGVVMTKIGGWVIDHYKLIGDIH 433 A+AHQ WS N+ TTV D+FP++ + +VVGIGG+AG +G + + G + Sbjct: 342 AAAHQGWSANLVTTVGDVFPRRMVGTVVGIGGVAGMIGSFFYSGVIGETLQ--------R 393 Query: 434 TG-YMIMFAICALAYLVAWSVMKALVPR 460 TG Y ++FA+ A AYLVA ++ L+PR Sbjct: 394 TGQYWVLFAVGASAYLVALGIIHLLMPR 421 Lambda K H 0.327 0.140 0.449 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: 750 Number of extensions: 41 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: 467 Length of database: 429 Length adjustment: 33 Effective length of query: 434 Effective length of database: 396 Effective search space: 171864 Effective search space used: 171864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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