Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate WP_057508914.1 ABB28_RS12315 glucose/galactose MFS transporter
Query= SwissProt::P11551 (438 letters) >NCBI__GCF_001431535.1:WP_057508914.1 Length = 438 Score = 269 bits (688), Expect = 1e-76 Identities = 152/399 (38%), Positives = 233/399 (58%), Gaps = 9/399 (2%) Query: 33 SLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIPIPAGILMKKLSYKA 92 ++FF+W LNDIL+P + F L +A L+Q F+ YF++ +PAG L+ L YK Sbjct: 31 TIFFMWGFLTCLNDILIPHLKAVFELNYARAMLVQFTFFGAYFLMSLPAGRLVAHLGYKK 90 Query: 93 GIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAANPFVTVLGPESSGH 152 GI+ GL + +GA FWPAAE+ Y+ FL LF++A G+ L+ AANP+V +LGP + Sbjct: 91 GIVAGLLIAGVGALGFWPAAELREYSAFLGALFVLATGITVLQVAANPYVALLGPVETSS 150 Query: 153 FRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLSAYKHSLVLSVQTPY 212 RL LAQ NS G IA +FG LIL N +S D ++ +S + +AY+ + SVQ PY Sbjct: 151 SRLTLAQALNSLGTAIAPIFGGLLILGNTV-KSADEINALSVAEQAAYRAAEAQSVQGPY 209 Query: 213 MIIVAIVLLVALLIMLTKFPAL--QSDNHSDAKQGSFSASLSRLARIRHWRWAVLAQFCY 270 + + ++L+AL + L + P L ++ D Q S+ A+L R RH +AVL F Y Sbjct: 210 IGLAIALVLLALFVYLFRLPTLSESAEKVDDGPQQSYGAAL----RHRHLLFAVLGIFFY 265 Query: 271 VGAQTACWSYLIRY-AVEEIPGMTAGFAANYLTGTMVCFFIGRFTGTWLISRFAPHKVLA 329 VGA+ + S+L+ Y ++ I G T A +Y++ IGRF G+ L++R++P +LA Sbjct: 266 VGAEVSIGSFLVNYLSMPTIGGFTEQQATHYVSAYWTMAMIGRFAGSALLTRYSPRHMLA 325 Query: 330 AYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNLGQDTKYGSSFIVM 389 +A I + L + + G V L ++ F SI +PTIF+LGI+ LG T SS ++M Sbjct: 326 LFAGINVLLLGTTMASSGQVALYSVVAIGLFNSIMFPTIFALGIERLGPLTNKASSLLIM 385 Query: 390 TIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIF 428 I+GG +V + G ++D G P+ ++P LC+ + F Sbjct: 386 AIVGGALVPYLQGVLADHIGLQPSF-ILPLLCYGYVIFF 423 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: 466 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: 438 Length adjustment: 32 Effective length of query: 406 Effective length of database: 406 Effective search space: 164836 Effective search space used: 164836 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