Align L-fucose-proton symporter; 6-deoxy-L-galactose permease; L-fucose permease (characterized)
to candidate Echvi_3909 Echvi_3909 Fucose permease
Query= SwissProt::P11551 (438 letters) >FitnessBrowser__Cola:Echvi_3909 Length = 469 Score = 225 bits (574), Expect = 2e-63 Identities = 150/472 (31%), Positives = 226/472 (47%), Gaps = 84/472 (17%) Query: 14 VDKDAGQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQAGLIQSAFY-- 71 V+ D+GQ Y+ P L+ LFF+W +NDIL+P QQ FTL N+QA LIQ+AF+ Sbjct: 15 VEFDSGQQ--YLGPLFLVTMLFFMWGFITCMNDILIPHLQQVFTLQNWQAMLIQTAFFGA 72 Query: 72 -----FGYFIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVGLFI 126 GY++I I G + ++ YK GII GL + A+G F+PAA ++++ FL LF+ Sbjct: 73 YFFISLGYYLISITKGDPIGRIGYKNGIILGLVISAVGCLFFYPAASLVSFGFFLFALFV 132 Query: 127 IAAGLGCLETAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPHQSQ 186 +A+G+ L+ AANP+VT+LG S RLN+ Q FNS G IA + G LI + Sbjct: 133 LASGITILQIAANPYVTILGKPSGASSRLNMTQAFNSLGTTIAPLIGGYLIFGAI----- 187 Query: 187 DVLDKMSPEQLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAKQGS 246 +SA SV+ PY+ + +LL+AL+ L K P + S + G+ Sbjct: 188 ------GDVDISAD------SVKMPYVALALTLLLIALIFKLFKLPEIGSQGVIISDSGA 235 Query: 247 FSASLSRLARIRHWRWAVLAQFCYVGAQTACWSYLIRYA-VEEIPGMTAGFAANYLTGTM 305 + RH + A F YVG + S LI +A + EI G+ A++YL Sbjct: 236 L--------KHRHLMLGIGAIFAYVGGEVTVGSNLINFARLPEIAGLDEAEASHYLALFW 287 Query: 306 VCFFIGRFTG-------------------------------------------------T 316 +GRF G Sbjct: 288 GGAMVGRFFGAVALADFKHNLNRFLIIGAITAISYVTIYYVYGGEMALYALAFIGLNIVV 347 Query: 317 WLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMSIQYPTIFSLGIKNL 376 +I +F P++ L + + + L +I G + L ++ F SI +PTIFSL IK L Sbjct: 348 IIIGQFIPNRTLWLFGITGIGLLVIGLLTSGQLALWSIVALGLFNSIMFPTIFSLAIKGL 407 Query: 377 GQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCFAVIFIF 428 G+ T SS +VM I+GG IV + G ++D +G++ + L+P C+ I + Sbjct: 408 GKYTAQASSLLVMAIVGGAIVPLLQGLLADISGSVQLSFLVPLACYLYIVFY 459 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: 495 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 438 Length of database: 469 Length adjustment: 33 Effective length of query: 405 Effective length of database: 436 Effective search space: 176580 Effective search space used: 176580 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