Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate 7025147 Shewana3_2310 glucose/galactose transporter (RefSeq)
Query= reanno::SB2B:6936374 (413 letters) >FitnessBrowser__ANA3:7025147 Length = 423 Score = 420 bits (1080), Expect = e-122 Identities = 223/416 (53%), Positives = 291/416 (69%), Gaps = 17/416 (4%) Query: 1 MAFVSSTTPQNGSAAPA-QSHQQLLFGAMTSLFFIWGFITALNDILIPHLKGIFDLSYTQ 59 MA +T+ S + A + + ++TSLFF+WGFIT LNDILIPHLK +F L+YTQ Sbjct: 1 MASSINTSSHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQ 60 Query: 60 AMLVQFCFFGAYFLVSPLAGVLIARIGYLRGIIFGLSTMATGCLLFYPASSLEQYALFLL 119 AML+QFCFFGAYFLVS AG L+ R+GY +GI+ GL + GC LFYPA+S Y LFL Sbjct: 61 AMLIQFCFFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLG 120 Query: 120 ALFVLASGITILQVSANPFVARLGPERTAASRLNLAQALNSLGHTLGPLFGSLLIFGAAA 179 ALFVLASGITILQV+ANP+V LG TA+SRLNL QA N+LG T+ P FGS+LI AA Sbjct: 121 ALFVLASGITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAA 180 Query: 180 GTH----------EAVQLPYLLLAAVIGIIAVGFIFLGGKV--KHADMGVD----HRHKG 223 E V+LPYLLLAA + ++A+ F L V +H+ + H K Sbjct: 181 SVSSELAQANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKT 240 Query: 224 SLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEKSAAELVSWYWGGAMIG 283 S L L+LGA+ IF+YVGAEVSIGSFLVN+ E I G+ E+ AA +++YWGGAM+G Sbjct: 241 SALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVG 300 Query: 284 RFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVLAVGFFNSIMFPTIFTL 343 RF G+A+ ++ VLA NA A LL+++ + +SG +A+ A+L VG FNSIMFPTIF+L Sbjct: 301 RFIGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSL 360 Query: 344 AIEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFIVPTFCYFYICWY 399 A+ LG TS+GSG+LC AIVGGA++P++QGV+ADN+G+QL+FI+P CY +I +Y Sbjct: 361 ALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFY 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: 496 Number of extensions: 20 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: 423 Length adjustment: 32 Effective length of query: 381 Effective length of database: 391 Effective search space: 148971 Effective search space used: 148971 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