Align Glucose/galactose porter (characterized)
to candidate WP_109739303.1 C1634_RS24670 L-fucose:H+ symporter permease
Query= TCDB::P0C105 (412 letters) >NCBI__GCF_002899945.2:WP_109739303.1 Length = 414 Score = 237 bits (604), Expect = 5e-67 Identities = 135/410 (32%), Positives = 218/410 (53%), Gaps = 18/410 (4%) Query: 11 LHTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGA 70 ++T ++K Y L + LFF W + D+L H +NV +++ ++S L+Q FGA Sbjct: 1 MNTTKFTEKKYYVVLAFVISLFFFWAIALTMGDVLNKHFQNVLKISKSESGLVQLSIFGA 60 Query: 71 YFIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTI 130 Y ++ +PAG +KR YK G+++GL + A+G LFIPAA+ + F ALFVLA G+ Sbjct: 61 YALMGIPAGLFMKRFGYKLGVILGLSLFALGSFLFIPAANQISFNFFRIALFVLAMGMAT 120 Query: 131 LQVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAATDATVNAEADAV 190 L+ A+P+V LG +T+ R+ Q+FN LG + P+ G I + + D+V Sbjct: 121 LETVAHPFVAALGNEKTSDQRVNFAQSFNGLGAIIGPLLGGFFIFGRS--GLEDNSLDSV 178 Query: 191 RFPYLLLALAFTVLAIIFAILKPP---DVQEDEPALSDKKEG----------SAWQYRHL 237 + Y + + + IIF+ +K P D E +SD ++G ++ RH Sbjct: 179 KNLYTWIGIVILTITIIFSFIKVPSLKDTHAGEIQISDSEKGVEADVSDPHAPLYKQRHF 238 Query: 238 VLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAM 297 + I F + A+ ++ +N+ + L E A+++ + M+GRF+G+ M Sbjct: 239 IFAVIAQFFNIAAQGGTWAYFINYGVEK--MNLPEIQASYYFSLSMAMMMIGRFVGTFLM 296 Query: 298 RYIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSH 357 ++I K LA I+L I + G ++ S++ + LF S+M+PTIFSL L LGS Sbjct: 297 KFIAPNKLLAIFTACNIVLCLIISQSFGWVSFMSLILLNLFLSVMYPTIFSLGLKRLGSK 356 Query: 358 TSQGSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFYGL 407 Q S L +A+ GGAI P + G +A+ H A+L+PIICYA I + L Sbjct: 357 VPQASSFLVMAMFGGAIFPPLMGKIAEKDIAH-AYLLPIICYAVILLFAL 405 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: 499 Number of extensions: 24 Number of successful extensions: 6 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: 414 Length adjustment: 31 Effective length of query: 381 Effective length of database: 383 Effective search space: 145923 Effective search space used: 145923 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: 50 (23.9 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