Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate N515DRAFT_1222 N515DRAFT_1222 MFS transporter, FHS family, L-fucose permease
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__Dyella79:N515DRAFT_1222 Length = 422 Score = 249 bits (635), Expect = 1e-70 Identities = 159/414 (38%), Positives = 213/414 (51%), Gaps = 29/414 (7%) Query: 13 SAAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYF 72 S++ A L + SLFF+WG LND+LIP K F L+ QA LVQ F+ YF Sbjct: 4 SSSRAAGRSPLPLALIVSLFFLWGVANNLNDVLIPQFKKAFVLNDFQAGLVQSAFYLGYF 63 Query: 73 LVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQ 132 LV+ AG+ + R GY ++FGL+ G LLF+PA+ Y FL ALFV+ASG+ L+ Sbjct: 64 LVAMPAGIYMRRFGYKSAVVFGLALYGLGALLFWPAAQQGTYGFFLFALFVIASGLAFLE 123 Query: 133 VSANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAAAGTHE--------- 183 SANPFV LGP +AA RLNLAQA N LG G L G IF T E Sbjct: 124 TSANPFVTLLGPRESAARRLNLAQAFNPLGSITGILIGQHFIFSGVEHTPEQLAALSAAE 183 Query: 184 ----------AVQLPYLLLAAVIGIIAVGFIFLGGK------VKHADMGVDHRHKGSLLS 227 AVQLPYL + V ++A G + L + V+ + DH LL Sbjct: 184 RAAFVAHETAAVQLPYLAIGLV--VLAWGLLILLTRFPAVHAVEEGAVPRDHGALARLLG 241 Query: 228 HKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIGRFAG 287 +R L A F YVGA+V + S+L+ Y + ++ G K AA + M GRFAG Sbjct: 242 DRRFLATLAAQFFYVGAQVGVWSYLIRY-VQATMPGTPAKLAANYMLVSLACFMAGRFAG 300 Query: 288 AALTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTLAIEG 347 +AL R P +LA A L + + G A++A FF S+M+PTIF L +EG Sbjct: 301 SALMRYVAPRRLLALFAAVNVALTVFAVAVPGVAGACALVACSFFMSVMYPTIFALGVEG 360 Query: 348 LGELTSR-GSGLLCQAIVGGALLPVIQGVVADNVGVQLSFIVPTFCYFYICWYA 400 G+ + GS LL I+GGA+L G V+D G+ + +VP + I +A Sbjct: 361 RGDDERKLGSALLVMTIIGGAVLTAAMGAVSDAAGISRAMLVPAASFVVILLFA 414 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: 486 Number of extensions: 19 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: 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 Apr 09 2024. 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