Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate 6937507 Sama_1663 glucose/galactose transporter (RefSeq)
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__SB2B:6937507 Length = 415 Score = 419 bits (1078), Expect = e-122 Identities = 215/380 (56%), Positives = 280/380 (73%), Gaps = 9/380 (2%) Query: 27 AMTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIARIG 86 ++T+LFF+WGFIT LNDILIPHLK +F L+Y QAML+QFCFFGAYFLVS AGVL+ R+G Sbjct: 26 SLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQAMLIQFCFFGAYFLVSVPAGVLVKRLG 85 Query: 87 YLRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGPER 146 Y +GI+ GL T A GC LFYPA+ Y +FL ALFVLASGIT+LQV+ANP+V LGP + Sbjct: 86 YQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGALFVLASGITVLQVAANPYVTALGPVQ 145 Query: 147 TAASRLNLAQALNSLGHTLGPLFGSLLIFGAAAGTH-----EAVQLPYLLLAAVIGIIAV 201 TA+SRL L QA NSLG T+ P FGS+LI A G +AV+LPYLLL ++ ++AV Sbjct: 146 TASSRLTLTQAFNSLGTTIAPAFGSVLILSVAVGASAEAEADAVKLPYLLLCGMLIVLAV 205 Query: 202 GFIFLGGKVKHADMGVDH--RHKGSLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEP 259 F L K+ H D S L+H+ L+LGA+ IF+YVG EV+IGSFLVN+ E Sbjct: 206 VFALL--KLPHIHDQEDEVAATGQSALAHRHLVLGAIGIFVYVGGEVAIGSFLVNFLGES 263 Query: 260 SIGGLDEKSAAELVSWYWGGAMIGRFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSG 319 + G+ E AA +++YWGGAM+GRF GAA+ ++ + VL NA A LL+++ + SSG Sbjct: 264 HVAGMAEADAAHYIAFYWGGAMVGRFIGAAVMQKVDAGKVLGFNATMAALLVLVAMNSSG 323 Query: 320 ELALVAVLAVGFFNSIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADN 379 LA+ A+LAVG FNSIMFPTIF+LA++ LG T++GSG+LC AIVGGAL+P++QG++AD+ Sbjct: 324 ALAMWAILAVGLFNSIMFPTIFSLALKNLGPATAQGSGILCLAIVGGALVPLLQGLLADS 383 Query: 380 VGVQLSFIVPTFCYFYICWY 399 VG+ SFI+P CY YI +Y Sbjct: 384 VGLSASFILPVLCYGYILFY 403 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: 514 Number of extensions: 19 Number of successful extensions: 2 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: 415 Length adjustment: 31 Effective length of query: 382 Effective length of database: 384 Effective search space: 146688 Effective search space used: 146688 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