Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate CA265_RS08575 CA265_RS08575 L-fucose:H+ symporter permease
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__Pedo557:CA265_RS08575 Length = 422 Score = 244 bits (622), Expect = 5e-69 Identities = 152/402 (37%), Positives = 221/402 (54%), Gaps = 29/402 (7%) Query: 23 LLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLI 82 L F + SLFF+WG L+ ILIPHLK +L+ Q+ L+ F AYFL++ AG+++ Sbjct: 15 LPFILVISLFFLWGMAHNLDSILIPHLKKACNLNNRQSTLIDTSVFFAYFLMAIPAGMIL 74 Query: 83 ARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARL 142 + GY +I GL A G LF PA++ Y FL+ALF++ G+T+L+ SANP+ A L Sbjct: 75 KKWGYKATMISGLLAFAFGAFLFVPAANNLSYITFLIALFIIGCGLTMLETSANPYAAVL 134 Query: 143 GPERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAAAGTHE------------------- 183 G A SRLNLA + N L + P+ G L I + T E Sbjct: 135 GDPAKATSRLNLAASFNGLAAMVAPMIGGLFILSGKSHTKEELAAMTDAGRNSYFLEEAA 194 Query: 184 AVQLPYLLLAAVIGIIAVGFIFLG-GKVKHADMGVDHRHKGSL---LSHKRLLLGALAIF 239 +V+ PY+ L V+ +IA F F+ ++K +D KGS L HK L +A F Sbjct: 195 SVKTPYITLGIVLLVIAAIFYFIHLPEIK--TKSIDGEAKGSFFGALRHKHLKWAVVAQF 252 Query: 240 LYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGRFAGAALTRRFNPAMV 299 YVGA+V + SF + + GG DEK+AA ++ Y +GRFAG A+ + + + Sbjct: 253 FYVGAQVCVTSFFIRMAQQG--GGFDEKTAASYLAIYGLLFTVGRFAGTAILQFVSSHKL 310 Query: 300 LAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEGLGELTSRGSGLL 359 LA AV + LL ++ I+ G + A+ A+GFF SIMFPTIF L I+G+G+ T GS L Sbjct: 311 LAIYAVISILLCLVAILGKGSYVVYALGAIGFFMSIMFPTIFALGIDGIGDDTKPGSSWL 370 Query: 360 CQAIVGGALLPVIQGVVADNVG--VQLSFIVPTFCYFYICWY 399 +IVGGA+LP G + D G +Q+ + +P C+ I ++ Sbjct: 371 IMSIVGGAILPFGMGSLIDMYGDNIQIGYSIPLVCFLVILYF 412 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: 484 Number of extensions: 28 Number of successful extensions: 3 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: 422 Length adjustment: 32 Effective length of query: 381 Effective length of database: 390 Effective search space: 148590 Effective search space used: 148590 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