Align L-fucose permease (characterized, see rationale)
to candidate Echvi_0508 Echvi_0508 L-fucose:H+ symporter permease
Query= uniprot:G8JZT2 (438 letters) >FitnessBrowser__Cola:Echvi_0508 Length = 431 Score = 360 bits (923), Expect = e-104 Identities = 186/427 (43%), Positives = 278/427 (65%), Gaps = 17/427 (3%) Query: 4 TKQSIISKDGVSYLIPFILITSCFALWGFANDITNPMVKAFSKIFRMSATDGALVQVAFY 63 +K +++SK + L PFIL+TS F LWG AN++T+ ++ AF KI M+ T + +Q+AFY Sbjct: 5 SKSALVSK---ATLWPFILLTSLFLLWGLANNMTDTLLAAFKKILSMTDTQTSFIQLAFY 61 Query: 64 GGYFAMAFPAAMFIRKFSYKAGVLLGLGLYAFGAFLFFPAKMTGEYYPFLIAYFILTCGL 123 G YF +A PAA++I+K++YK+GVLLGLGL+A G LF+PA +T Y FL A ++L GL Sbjct: 62 GAYFCLALPAAIYIKKYTYKSGVLLGLGLFAVGGLLFYPASITMSYGFFLFALYVLAGGL 121 Query: 124 SFLETSCNPYILSMGTEETATRRLNLAQSFNPMGSLLGMYVAMQFIQAKLHPMGTDERAL 183 S LETS NPYI+ MG E +ATRRLNLAQSFNP+GS++G+ ++ FI +KL+ DER+ Sbjct: 122 SILETSANPYIMVMGPEASATRRLNLAQSFNPVGSIIGVVLSKFFILSKLNVAEADERSR 181 Query: 184 LNDSEFQAIKESDLAVLIAPYLIIGLVILAMLLLIRFVKMPKNGDQNHKIDFFPTLKRIF 243 + + Q +++ +L ++ Y+ + L ++ M +LI+F KMP + + LKR+ Sbjct: 182 MTAEQLQQVRQEELDAVMGTYVGVALFLVVMWVLIKFTKMPTASEGGLQDSLGNGLKRLL 241 Query: 244 TQTRYREGVIAQFFYVGVQIMCWTFIIQYGTRLFMSPEYGMDEKSAEVLSQQYNIVAMVI 303 Y GV+AQFFYVG QI W++ I+Y + E M+E A Y + A+V+ Sbjct: 242 GNKNYVFGVLAQFFYVGAQIGIWSYTIRY-----VMMELDMNESDA----SNYYLAAIVL 292 Query: 304 FCISRFICTFILRYLNAGKLLMILAIFGGIFTLGTIFLQNIFGLYCLVAVSACMSLMFPT 363 F +SRF+ T +++++ L+ I AI T+ IF + G LV +S CMSLMFPT Sbjct: 293 FTVSRFLFTALMKFVRPSLLMAISAIGAIGLTMVVIFGHGMVGSIALVCISGCMSLMFPT 352 Query: 364 IYGIALKGMGDDAKFGAAGLIMAILGGSVLPPLQASIIDMKEIASMPAVNVSFILPLTCF 423 IYG+A +G+GDD K G +GLIMAILGG++ P +Q + D S+ ++++SF +P C+ Sbjct: 353 IYGLAAEGLGDDTKLGGSGLIMAILGGAIFPFIQGLVSD-----SLDSIHLSFFVPAACY 407 Query: 424 LVIIGYG 430 LV++ YG Sbjct: 408 LVVVAYG 414 Lambda K H 0.331 0.144 0.439 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: 537 Number of extensions: 22 Number of successful extensions: 5 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: 431 Length adjustment: 32 Effective length of query: 406 Effective length of database: 399 Effective search space: 161994 Effective search space used: 161994 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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