Align Glucose/galactose porter (characterized)
to candidate WP_009134173.1 HMPREF9450_RS06960 L-fucose:H+ symporter permease
Query= TCDB::P0C105 (412 letters) >NCBI__GCF_000231275.1:WP_009134173.1 Length = 441 Score = 188 bits (477), Expect = 3e-52 Identities = 121/407 (29%), Positives = 201/407 (49%), Gaps = 29/407 (7%) Query: 28 LTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIVSLPAGQLVKRISY 87 +T LFF WGF + + ++ +F+++ T L+Q F+G YF ++ PA +++ SY Sbjct: 19 VTSLFFAWGFANDITNPMVKAFSKIFRMSTTDGALVQLAFYGGYFAMAFPAALFIRKFSY 78 Query: 88 KRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVAANPYVTILGKPET 147 K GI+VGL + A G +FIPA+ +Y FL A F+L G++ L+ ++NPY+ +G T Sbjct: 79 KSGILVGLALYACGALMFIPASKTGLYFPFLIAYFILTCGLSFLETSSNPYILSMGDEST 138 Query: 148 AASRLTLTQAFNSLGTTVAPVFGAVLILSAAT----------------DATVNAEADAVR 191 A RL L+QAFN +G+ + +F A+ + A +A A+ + + Sbjct: 139 ATRRLNLSQAFNPIGSLLG-MFCAMQFIQARMSPLDTAERAQLSDAEFEAVKAADLNVLI 197 Query: 192 FPYLLLALAFTVL-AIIFAILKPPDVQEDEPALSDKKEGSAWQYRHLVLGAIGIFVYVGA 250 PY+++ L L +IF P + +D + W G I F YVGA Sbjct: 198 TPYVIVGLVILALFFLIFFTKMPKNGDKDHSMNLGRVLKRIWAIPRYREGVIAQFFYVGA 257 Query: 251 EVSVGSFLVNFLSDP-TVAGLSETDAAHHVAYFWGGAM----VGRFIGSAAMRYIDDGKA 305 ++ +F++ + + T G+ E A + AM V RFI + M+Y G Sbjct: 258 QIMCWTFIIQYGTRVFTQTGMEEQAAEVLSQRYNIVAMAIFCVSRFICTFLMKYFSPGAL 317 Query: 306 LAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHTSQGSGIL 365 L A L + M+ ++ + S+MFPTI+ +AL GLG G+ L Sbjct: 318 LMTFAIAGSALTAGVIGFQNINGMYCLVGVSACMSLMFPTIYGIALEGLGDDAKFGAAGL 377 Query: 366 CLAIVGGAIVPLIQGALAD------AIGIHLAFLMPIICYAYIAFYG 406 +AI+GG+I+P Q A+ D ++++F++P+IC+ I YG Sbjct: 378 IMAILGGSIMPPAQAAIIDQGMLFGLPAVNVSFILPLICFLVIIVYG 424 Lambda K H 0.328 0.141 0.420 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: 538 Number of extensions: 32 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: 412 Length of database: 441 Length adjustment: 32 Effective length of query: 380 Effective length of database: 409 Effective search space: 155420 Effective search space used: 155420 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 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