Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate BPHYT_RS30935 BPHYT_RS30935 MFS transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__BFirm:BPHYT_RS30935 Length = 439 Score = 221 bits (564), Expect = 3e-62 Identities = 134/438 (30%), Positives = 215/438 (49%), Gaps = 28/438 (6%) Query: 14 LLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQIPGGWLLDR 73 L +L + +NY DR T+A+A ++ DLG+ +G + SAF W+Y Q+P G L+DR Sbjct: 22 LTLLMVSGIVNYLDRGTLAVANPLIRHDLGLSLGEMGLLLSAFSWSYALFQLPVGGLVDR 81 Query: 74 FGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFPGNARIVAA 133 G +K+ + + WSL G+V FG + R ++G+ EAP FP AR+V+ Sbjct: 82 IGPRKLLGIGLIVWSLAQASGGFVSTFGW------FILARIVLGIGEAPQFPSAARVVSN 135 Query: 134 WFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIFSLIWLKVI 193 WFP RG + IFNSA T L + +V F W+ FIV GV+G++ +L+WL V Sbjct: 136 WFPLRARGKPTGIFNSASPLGTALAPLCLSVLVVQFHWRWAFIVTGVVGLVVALVWLAVY 195 Query: 194 HSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNRMMLGVYLGQ 253 P + M EAE +++ + D D+ +W R L ++ G+ +G Sbjct: 196 RDPVKATM-TEAERHYLEGD------DADRKPAPTVTFAEW---RSLFSHGTTWGMLIGF 245 Query: 254 YCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISDYLLRKGHS 313 + + + +LTW P YL +R M+++ G AS+P CGF+G + G SD + + S Sbjct: 246 FGSVYLNWVYLTWLPGYLTMERHMSLMHTGVAASIPFFCGFLGSLTAGWFSDLITSRSTS 305 Query: 314 LTFARKAPIIGGLL------ISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAVVSD 367 +R+ ++ +L I +++V N + +V + F A WA+ + Sbjct: 306 PVASRRNAVVIAMLGMVAFTIPAALVESNTI----AIVCISVVIFLANAASASSWALATA 361 Query: 368 TSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSYLVI 427 +P G G + N G L PI+ GY I+ + SF AL+ A + SYL++ Sbjct: 362 AAPPNRVGSLGAIQNFGGFLGGALAPILTGY-IAQSWSFVPALLTAAGIAFIGAMSYLLL 420 Query: 428 V-GPIKRVVLKEPPTQGP 444 V PI+ P + P Sbjct: 421 VRKPIEDPSTPTEPVRAP 438 Lambda K H 0.327 0.142 0.444 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: 659 Number of extensions: 40 Number of successful extensions: 7 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: 454 Length of database: 439 Length adjustment: 33 Effective length of query: 421 Effective length of database: 406 Effective search space: 170926 Effective search space used: 170926 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