Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate WP_091369124.1 BLU33_RS03105 L-fucose:H+ symporter permease
Query= SwissProt::P11551 (438 letters) >NCBI__GCF_900105165.1:WP_091369124.1 Length = 410 Score = 273 bits (698), Expect = 7e-78 Identities = 154/416 (37%), Positives = 235/416 (56%), Gaps = 23/416 (5%) Query: 16 KDAGQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYF 75 K A Y + + +LF LW +A L D+L FQ ++ +GL+Q + + Y Sbjct: 4 KPAFTEPKYRVILFFVTALFMLWGIAITLGDVLNRHFQNVLHISKSHSGLVQLSIFGAYA 63 Query: 76 IIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLE 135 ++ IPAG+ MK+ YK GI+ GLFLYA GA LF PAA+ +++ F + LFI+A GL LE Sbjct: 64 VMGIPAGLFMKRFGYKKGILLGLFLYAFGAFLFVPAADAVSFDFFRIALFILACGLATLE 123 Query: 136 TAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPE 195 T A+PFV LG + + R+N +Q FN G +I G IL S D Sbjct: 124 TVAHPFVAALGDQRTSDQRINFSQAFNGLGGVIGPTLGGYFILKGQQIHSND-------- 175 Query: 196 QLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHS--DAKQGSFSASL-S 252 +++V+ Y+II ++++L+ +L + K P L ++ D + + + Sbjct: 176 ---------LIAVKYLYVIIGSVIVLIGVLFLFLKVPHLTHAHNEVIDYENAEGNKKIEK 226 Query: 253 RLARIRHWRWAVLAQFCYVGAQTACWSYLIRYAVEEIPGMTAGFAANYLTGTMVCFFIGR 312 +L +H+ +AV+AQF V AQ W+Y I Y E+ ++ AA + + +M+ IGR Sbjct: 227 KLIHQKHYVFAVVAQFFNVAAQGGTWAYFINYG-HEMVHLSDERAAYFFSLSMIMLMIGR 285 Query: 313 FTGTWLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLG 372 FTGT+L+ AP+++L+ +A + +CLI A G + IAL + F SI +PTIFSLG Sbjct: 286 FTGTFLMRYIAPYRLLSIFAAANIVMCLIVAQGAGWLSFIALLFINFFFSIMFPTIFSLG 345 Query: 373 IKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIF 428 +KNLG T+ GSSFIVM +IGGG+ P+MG + A +I A +P +C+ VIF+F Sbjct: 346 LKNLGGKTQQGSSFIVMGVIGGGLFPPLMGLI--ANHDIAAAYYLPIICYIVIFLF 399 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: 485 Number of extensions: 25 Number of successful extensions: 4 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: 410 Length adjustment: 32 Effective length of query: 406 Effective length of database: 378 Effective search space: 153468 Effective search space used: 153468 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 24 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