Align Glucose/galactose transporter (characterized, see rationale)
to candidate N515DRAFT_0592 N515DRAFT_0592 glucose/galactose transporter
Query= uniprot:A0KXM0 (423 letters) >FitnessBrowser__Dyella79:N515DRAFT_0592 Length = 430 Score = 220 bits (561), Expect = 6e-62 Identities = 142/430 (33%), Positives = 230/430 (53%), Gaps = 19/430 (4%) Query: 6 NTSSHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQ 65 +TS + +G ++ L LFF++GF+T LN LI +K FSL+ A L+ Sbjct: 3 STSFAAGDTHDRASGLVPMLIIGL--LFFIFGFVTWLNGPLITFVKLAFSLDDVNAFLVP 60 Query: 66 FCFFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVL 125 F+ +YF +++P+ ++KR G +KG+ GL + +IG LF S YG L LFV+ Sbjct: 61 MVFYCSYFFLALPSSAVLKRTGMKKGMALGLFVMAIGAVLFGQFVSMRVYGGALAGLFVI 120 Query: 126 ASGITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILS-------- 177 +G+ +LQ A+NPY++ LG ++A+ R+ N + +APF L+LS Sbjct: 121 GAGLALLQTASNPYISILGPIDSAAQRIAFMGICNKVAGALAPFVFGWLVLSGIDTFDQQ 180 Query: 178 VAASVSSELAQA--NAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQT 235 V A+ + E +A N A V +PYL +A L +LA+ + LP I+ A E + Sbjct: 181 VKAAPTPEAREALLNTFAAKVHMPYLAMAGLLVLLAVWVLRSPLPEIK--PSGANSEAEI 238 Query: 236 HLGKTSALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWG 295 K + L HL LG + +F+YVG EV G + + G+ +G+P + H+ ++ Sbjct: 239 GHAKGNLLSFPHLWLGVLCLFLYVGVEVMAGDAIGTY-GQG--LGLPLDATKHFTSFTLF 295 Query: 296 GAMVGRFIGSAVMQK-IPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMF 354 ++G G ++ K I + LA +A + + A T+G ++ + +G N++M+ Sbjct: 296 AMLLGYLAGLVLIPKIISQQSYLAVSAVLGVAFTVGAWATTGYTSVGFVAALGFANAMMW 355 Query: 355 PTIFSLALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVV-CYGFI 413 P IF LA++ LG T GS +L +AIVGGA+VP L + QL F+L +V CY +I Sbjct: 356 PAIFPLAIKGLGRWTEAGSALLIMAIVGGALVPQAFVHLKQHYDFQLVFMLLMVPCYLYI 415 Query: 414 LFYGAKGSKM 423 LFYG +G ++ Sbjct: 416 LFYGLRGHRV 425 Lambda K H 0.326 0.138 0.402 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: 34 Number of successful extensions: 4 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: 423 Length of database: 430 Length adjustment: 32 Effective length of query: 391 Effective length of database: 398 Effective search space: 155618 Effective search space used: 155618 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 (21.7 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