Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate 5209419 Shew_1890 glucose/galactose transporter (RefSeq)
Query= SwissProt::P11551 (438 letters) >FitnessBrowser__PV4:5209419 Length = 421 Score = 239 bits (609), Expect = 2e-67 Identities = 142/415 (34%), Positives = 223/415 (53%), Gaps = 20/415 (4%) Query: 19 GQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFYFGYFIIP 78 G+ +Y L SLFF+W LNDIL+P + AF+L +A LIQ F+ YF++ Sbjct: 15 GEQENYRFALVSLTSLFFMWGFITCLNDILIPHLKAAFSLNYAEAMLIQFCFFGAYFLVS 74 Query: 79 IPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFIIAAGLGCLETAA 138 +PAG L+K L Y+ GI+TGL + ALG ALF+PAA + Y LFL LF++A+G+ L+ AA Sbjct: 75 MPAGKLVKALGYQKGIVTGLLIAALGCALFYPAAALATYGLFLGALFVLASGITILQVAA 134 Query: 139 NPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQDVLDKMSPEQLS 198 NP+V LG + RLNL Q FN+ G +A FG LILS S+ + + ++ Sbjct: 135 NPYVNALGSVETASSRLNLTQAFNALGTTVAPYFGAVLILSVAVEASETLTQAQAEAEV- 193 Query: 199 AYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPAL----QSDNHSDAKQGSFSASLSRL 254 V+ PY+I+ + ++AL+ P + QS + +++L L Sbjct: 194 ---------VKLPYLILATALGVLALVFAKLDLPQIKEHCQSGEQGEVVHNGKTSALQSL 244 Query: 255 ARIRHWRWAVLAQFCYVGAQTACWSYLIRY-AVEEIPGMTAGFAANYLTGTMVCFFIGRF 313 H + F YVGA+ + S+L+ + A ++I G++ AA+Y+T +GRF Sbjct: 245 ----HLVLGAVGIFVYVGAEVSIGSFLVNFLAQDDIAGLSEASAASYITYYWGGAMVGRF 300 Query: 314 TGTWLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGI 373 G+ ++ + VL AL+A L ++ + G V + A+ F SI +PTIFSL + Sbjct: 301 IGSAVMQKVPAGTVLGFNALMAALLVALAMTSTGTVAMWAILAVGLFNSIMFPTIFSLAL 360 Query: 374 KNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIF 428 ++LG T GS + + I+GG I+ + G ++D G I A +P +C+ I + Sbjct: 361 RDLGPHTSQGSGVLCLAIVGGAILPLLQGVLADNIG-IQHAFFLPIICYLFIMFY 414 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: 456 Number of extensions: 30 Number of successful extensions: 3 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: 421 Length adjustment: 32 Effective length of query: 406 Effective length of database: 389 Effective search space: 157934 Effective search space used: 157934 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