Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate BWI76_RS22920 BWI76_RS22920 MFS transporter
Query= SwissProt::P11551 (438 letters) >FitnessBrowser__Koxy:BWI76_RS22920 Length = 436 Score = 817 bits (2110), Expect = 0.0 Identities = 406/438 (92%), Positives = 425/438 (97%), Gaps = 2/438 (0%) Query: 1 MGNTSIQTQSYRAVDKDAGQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTN 60 MGNT+IQTQS+RAV+ G+S+ YIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTN Sbjct: 1 MGNTTIQTQSFRAVE--TGKSKRYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTN 58 Query: 61 FQAGLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLF 120 FQAGLIQSAFYFGYF+IPIPAGILMKKLSYKAGIITGLFLYA GAALFWPAAE+MNYTLF Sbjct: 59 FQAGLIQSAFYFGYFVIPIPAGILMKKLSYKAGIITGLFLYAFGAALFWPAAEVMNYTLF 118 Query: 121 LVGLFIIAAGLGCLETAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSN 180 L+GLFIIAAGLGCLETAANPFVTVLGPES GHFRLNLAQTFNSFGAIIAVVFGQSLILSN Sbjct: 119 LIGLFIIAAGLGCLETAANPFVTVLGPESGGHFRLNLAQTFNSFGAIIAVVFGQSLILSN 178 Query: 181 VPHQSQDVLDKMSPEQLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHS 240 VPHQSQDVLDKM+PEQLSAYKHSLVLSVQTPYMIIVA+VLLVALLIMLTKFPALQSD+HS Sbjct: 179 VPHQSQDVLDKMAPEQLSAYKHSLVLSVQTPYMIIVAVVLLVALLIMLTKFPALQSDDHS 238 Query: 241 DAKQGSFSASLSRLARIRHWRWAVLAQFCYVGAQTACWSYLIRYAVEEIPGMTAGFAANY 300 DA Q SFSASL+RL R+RHWRWAVLAQFCYVGAQTACWSYLIRYA+EEIPGMT GFAANY Sbjct: 239 DATQSSFSASLARLVRVRHWRWAVLAQFCYVGAQTACWSYLIRYAIEEIPGMTPGFAANY 298 Query: 301 LTGTMVCFFIGRFTGTWLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAF 360 LTGTMVCFFIGRF+GTWLISRFAPHKVLAAYAL++M LCLISAF GGHVGL+ALTLCSAF Sbjct: 299 LTGTMVCFFIGRFSGTWLISRFAPHKVLAAYALLSMILCLISAFTGGHVGLLALTLCSAF 358 Query: 361 MSIQYPTIFSLGIKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPAL 420 MSIQYPTIFSLGIKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAEL+PAL Sbjct: 359 MSIQYPTIFSLGIKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELVPAL 418 Query: 421 CFAVIFIFARFRSQTATN 438 CFAVIFIFARFRSQTA N Sbjct: 419 CFAVIFIFARFRSQTAAN 436 Lambda K H 0.329 0.140 0.425 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: 800 Number of extensions: 10 Number of successful extensions: 2 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: 438 Length of database: 436 Length adjustment: 32 Effective length of query: 406 Effective length of database: 404 Effective search space: 164024 Effective search space used: 164024 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 (21.8 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