Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate Echvi_0508 Echvi_0508 L-fucose:H+ symporter permease
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__Cola:Echvi_0508 Length = 431 Score = 219 bits (557), Expect = 2e-61 Identities = 138/410 (33%), Positives = 207/410 (50%), Gaps = 43/410 (10%) Query: 25 FGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIAR 84 F +TSLF +WG + D L+ K I ++ TQ +Q F+GAYF ++ A + I + Sbjct: 18 FILLTSLFLLWGLANNMTDTLLAAFKKILSMTDTQTSFIQLAFYGAYFCLALPAAIYIKK 77 Query: 85 IGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGP 144 Y G++ GL A G LLFYPAS Y FL AL+VLA G++IL+ SANP++ +GP Sbjct: 78 YTYKSGVLLGLGLFAVGGLLFYPASITMSYGFFLFALYVLAGGLSILETSANPYIMVMGP 137 Query: 145 ERTAASRLNLAQALNSLGHTLGPLFGSLLIFG---------------------------A 177 E +A RLNLAQ+ N +G +G + I A Sbjct: 138 EASATRRLNLAQSFNPVGSIIGVVLSKFFILSKLNVAEADERSRMTAEQLQQVRQEELDA 197 Query: 178 AAGTHEAVQLPYLLLAAVIGIIAVGFIFLGGKVKHADMGVDHRHKGSLLSHKRLLLGALA 237 GT+ V L +++ +I + GG G+ LL +K + G LA Sbjct: 198 VMGTYVGVALFLVVMWVLIKFTKMPTASEGGLQDSLGNGLKR-----LLGNKNYVFGVLA 252 Query: 238 IFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAM----IGRFAGAALTRR 293 F YVGA++ I S+ + Y ++E A+ Y+ A+ + RF AL + Sbjct: 253 QFFYVGAQIGIWSYTIRYVMMEL--DMNESDASN----YYLAAIVLFTVSRFLFTALMKF 306 Query: 294 FNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLGELTS 353 P++++A +A+ A L M+ I G + +A++ + S+MFPTI+ LA EGLG+ T Sbjct: 307 VRPSLLMAISAIGAIGLTMVVIFGHGMVGSIALVCISGCMSLMFPTIYGLAAEGLGDDTK 366 Query: 354 RGSGLLCQAIVGGALLPVIQGVVADNV-GVQLSFIVPTFCYFYICWYAFF 402 G L AI+GGA+ P IQG+V+D++ + LSF VP CY + Y F Sbjct: 367 LGGSGLIMAILGGAIFPFIQGLVSDSLDSIHLSFFVPAACYLVVVAYGLF 416 Lambda K H 0.329 0.142 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: 428 Number of extensions: 20 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: 413 Length of database: 431 Length adjustment: 32 Effective length of query: 381 Effective length of database: 399 Effective search space: 152019 Effective search space used: 152019 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: 50 (23.9 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