Align MFS transporter, FHS family, L-fucose permease (characterized, see rationale)
to candidate Echvi_0508 Echvi_0508 L-fucose:H+ symporter permease
Query= uniprot:A0A1I2JXG1 (442 letters) >FitnessBrowser__Cola:Echvi_0508 Length = 431 Score = 254 bits (649), Expect = 4e-72 Identities = 154/438 (35%), Positives = 247/438 (56%), Gaps = 19/438 (4%) Query: 9 PSKTSLPGAARERYTDYPMAMGVLTSIFFMWGFLTCLNDILIPHLKAVFKLNYAEAMLVQ 68 PSK++L A T +P + LTS+F +WG + D L+ K + + + +Q Sbjct: 4 PSKSALVSKA----TLWPFIL--LTSLFLLWGLANNMTDTLLAAFKKILSMTDTQTSFIQ 57 Query: 69 FTFFGAYFLMSLPAGLLVARLGYKKGIVAGLAVAGVGAAGFWPAAAMHFYPAFLGALFVL 128 F+GAYF ++LPA + + + YK G++ GL + VG F+PA+ Y FL AL+VL Sbjct: 58 LAFYGAYFCLALPAAIYIKKYTYKSGVLLGLGLFAVGGLLFYPASITMSYGFFLFALYVL 117 Query: 129 ATGITVLQVAANAYVALLGPEKSASSRLTLAQALNSLGTFLAPKFGGLLILSAA-VLSAE 187 A G+++L+ +AN Y+ ++GPE SA+ RL LAQ+ N +G+ + ILS V A+ Sbjct: 118 AGGLSILETSANPYIMVMGPEASATRRLNLAQSFNPVGSIIGVVLSKFFILSKLNVAEAD 177 Query: 188 QIAKLSPAEQVAYRVQEAQTVQGPYLGLAIVLFLLAVFVYLFRLPALTEKTEQASVKQHS 247 + ++++ + R +E V G Y+G+A+ L ++ V + ++P +E Q S+ + Sbjct: 178 ERSRMTAEQLQQVRQEELDAVMGTYVGVALFLVVMWVLIKFTKMPTASEGGLQDSL-GNG 236 Query: 248 LVSPLRHPHVLFGVLAIFFYVGGEVAIGSFLVNYLSMPDIGNMSEQAAANWVAYYWLGAM 307 L L + + +FGVLA FFYVG ++ I S+ + Y+ M +M+E A+N Y+L A+ Sbjct: 237 LKRLLGNKNYVFGVLAQFFYVGAQIGIWSYTIRYVMME--LDMNESDASN----YYLAAI 290 Query: 308 ----IGRFIGSALLAKLSPRKLLAIFAAINMALVLTTMMTKGTVAMYSVVSIGLFNSIMF 363 + RF+ +AL+ + P L+AI A + L + + G V ++V I S+MF Sbjct: 291 VLFTVSRFLFTALMKFVRPSLLMAISAIGAIGLTMVVIFGHGMVGSIALVCISGCMSLMF 350 Query: 364 PTIFSLGIERMGPMTGEASSLLIMAIVGGAIVPFVQGLFADHIGVQH-AFFLPLLCYAYI 422 PTI+ L E +G T S LIMAI+GGAI PF+QGL +D + H +FF+P CY + Sbjct: 351 PTIYGLAAEGLGDDTKLGGSGLIMAILGGAIFPFIQGLVSDSLDSIHLSFFVPAACYLVV 410 Query: 423 VFYGLYGSRIKSDTPVAA 440 V YGL+ + K + P A Sbjct: 411 VAYGLFHYKHKKEIPAMA 428 Lambda K H 0.327 0.140 0.414 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: 477 Number of extensions: 23 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: 442 Length of database: 431 Length adjustment: 32 Effective length of query: 410 Effective length of database: 399 Effective search space: 163590 Effective search space used: 163590 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 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