Align Glucose/galactose transporter (characterized, see rationale)
to candidate 5209419 Shew_1890 glucose/galactose transporter (RefSeq)
Query= uniprot:A0KXM0 (423 letters) >FitnessBrowser__PV4:5209419 Length = 421 Score = 658 bits (1698), Expect = 0.0 Identities = 331/403 (82%), Positives = 362/403 (89%) Query: 21 NYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYFLVSIPAG 80 NYRFALVSLTSLFFMWGFITCLNDILIPHLKA FSLNY +AMLIQFCFFGAYFLVS+PAG Sbjct: 19 NYRFALVSLTSLFFMWGFITCLNDILIPHLKAAFSLNYAEAMLIQFCFFGAYFLVSMPAG 78 Query: 81 QLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQVAANPYV 140 +LVK LGYQKGIVTGL+IA++GC LFYPAA+ ATYGLFLGALFVLASGITILQVAANPYV Sbjct: 79 KLVKALGYQKGIVTGLLIAALGCALFYPAAALATYGLFLGALFVLASGITILQVAANPYV 138 Query: 141 NALGSSETASSRLNLTQAFNALGTTVAPFFGSILILSVAASVSSELAQANAEAEVVKLPY 200 NALGS ETASSRLNLTQAFNALGTTVAP+FG++LILSVA S L QA AEAEVVKLPY Sbjct: 139 NALGSVETASSRLNLTQAFNALGTTVAPYFGAVLILSVAVEASETLTQAQAEAEVVKLPY 198 Query: 201 LLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSALQSMHLVLGAVGIFVYVG 260 L+LA AL VLA++FAKLDLP I+EH Q+ + H GKTSALQS+HLVLGAVGIFVYVG Sbjct: 199 LILATALGVLALVFAKLDLPQIKEHCQSGEQGEVVHNGKTSALQSLHLVLGAVGIFVYVG 258 Query: 261 AEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFIGSAVMQKIPAGTVLAFN 320 AEVSIGSFLVNFL + I G+ E AA YI YYWGGAMVGRFIGSAVMQK+PAGTVL FN Sbjct: 259 AEVSIGSFLVNFLAQDDIAGLSEASAASYITYYWGGAMVGRFIGSAVMQKVPAGTVLGFN 318 Query: 321 AFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALRDLGPHTSQGSGILCLAI 380 A MAALLV +AMT++G+VAMWAIL VGLFNSIMFPTIFSLALRDLGPHTSQGSG+LCLAI Sbjct: 319 ALMAALLVALAMTSTGTVAMWAILAVGLFNSIMFPTIFSLALRDLGPHTSQGSGVLCLAI 378 Query: 381 VGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKGSKM 423 VGGAI+PLLQGVLADN+GIQ AF LP++CY FI+FYG KGSK+ Sbjct: 379 VGGAILPLLQGVLADNIGIQHAFFLPIICYLFIMFYGVKGSKL 421 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: 647 Number of extensions: 19 Number of successful extensions: 1 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: 421 Length adjustment: 32 Effective length of query: 391 Effective length of database: 389 Effective search space: 152099 Effective search space used: 152099 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: 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