Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate 7025545 Shewana3_2696 major facilitator transporter (RefSeq)
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__ANA3:7025545 Length = 452 Score = 182 bits (461), Expect = 2e-50 Identities = 145/462 (31%), Positives = 235/462 (50%), Gaps = 66/462 (14%) Query: 1 MAFVSSTTPQNGSAAPAQSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQA 60 M F S +T +A+P S +L + LFF++GF+T LN LIP LK L+ +A Sbjct: 1 MKFTSDST--QATASPQGSFIPMLLIGI--LFFVFGFVTWLNGALIPFLKIACQLNEFEA 56 Query: 61 MLVQFCFFGAYFLVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLLA 120 LV F F+ AYF+++ ++ R+GY G+ GL MA G LF A+ + +A FLLA Sbjct: 57 YLVTFVFYIAYFVMALPTSSILTRLGYKMGMTLGLGIMAAGAGLFIVAALVGHFATFLLA 116 Query: 121 LFVLASGITILQVSANPFVARLGPERTAASRLNLAQALN-SLGHTLGPLFGSLLIFG--- 176 LFVL +G+T+LQ +ANP++ +GP +AA R++L +N G + +F + ++ G Sbjct: 117 LFVLGTGLTLLQTAANPYIVCIGPRESAAMRISLMGIVNKGAGFIVPIIFTAWILTGMEP 176 Query: 177 ----AAAGTHEAVQL------------PYLLLAAV-IGIIAVGFIF--------LGGKVK 211 A A EA + PYL++ V +G++A F++ LG +V+ Sbjct: 177 YSETALASLSEAQRQLALTELANRLVHPYLMMMLVLLGLMA--FVWFSPLPEPELGERVE 234 Query: 212 HADMGVDHRHKGSLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAE 271 D + ++L + +++LGAL +F YVGAEV G + F++ GL Sbjct: 235 RTQ--TDWK---AILQYPQVILGALTLFCYVGAEVIAGD-SIGLFSQ----GLGVAHFGM 284 Query: 272 LVSWYWGGAMIGRFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGE---------LA 322 + S+ G ++G G L R+ + A LL L ++ S L Sbjct: 285 MTSYTMGFMVLGYVLGILLIPRWISQQTALVGSAIAGLLFTLGVLLSDSQSQALSELLLG 344 Query: 323 LVAVLAV----------GFFNSIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGGALLPVI 372 + VL V G N++++P ++ LA+EGLG LT+ S LL I GGA+LP++ Sbjct: 345 WLGVLPVPDPVLYLALLGLANALVWPAVWPLALEGLGRLTATASALLIMGIAGGAILPLL 404 Query: 373 QGVVADNVG-VQLSFIVPTFCYFYICWYAFFARNRMNGETAS 413 G +A + G Q+++ + CY I +YA + +++ + AS Sbjct: 405 YGYIAHSQGDSQMAYFLLLPCYGLIFYYAIWG-HKLTAKVAS 445 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: 490 Number of extensions: 23 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: 452 Length adjustment: 32 Effective length of query: 381 Effective length of database: 420 Effective search space: 160020 Effective search space used: 160020 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: 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