Align Glucose/galactose transporter (characterized, see rationale)
to candidate WP_057508914.1 ABB28_RS12315 sugar MFS transporter
Query= uniprot:A0KXM0 (423 letters) >NCBI__GCF_001431535.1:WP_057508914.1 Length = 438 Score = 430 bits (1105), Expect = e-125 Identities = 223/412 (54%), Positives = 294/412 (71%), Gaps = 11/412 (2%) Query: 21 NYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYFLVSIPAG 80 N R AL T++FFMWGF+TCLNDILIPHLKAVF LNY +AML+QF FFGAYFL+S+PAG Sbjct: 21 NTRMALGVATTIFFMWGFLTCLNDILIPHLKAVFELNYARAMLVQFTFFGAYFLMSLPAG 80 Query: 81 QLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQVAANPYV 140 +LV LGY+KGIV GL+IA +G F+PAA Y FLGALFVLA+GIT+LQVAANPYV Sbjct: 81 RLVAHLGYKKGIVAGLLIAGVGALGFWPAAELREYSAFLGALFVLATGITVLQVAANPYV 140 Query: 141 NALGSSETASSRLNLTQAFNALGTTVAPFFGSILILS---------VAASVSSELAQANA 191 LG ET+SSRL L QA N+LGT +AP FG +LIL A SV+ + A A Sbjct: 141 ALLGPVETSSSRLTLAQALNSLGTAIAPIFGGLLILGNTVKSADEINALSVAEQAAYRAA 200 Query: 192 EAEVVKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAEEVQTHLGKTSALQSMHLVLG 251 EA+ V+ PY+ LA AL +LA+ LP + E ++ + Q G +AL+ HL+ Sbjct: 201 EAQSVQGPYIGLAIALVLLALFVYLFRLPTLSESAEKVDDGPQQSYG--AALRHRHLLFA 258 Query: 252 AVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFIGSAVMQKI 311 +GIF YVGAEVSIGSFLVN+L I G E+QA HY++ YW AM+GRF GSA++ + Sbjct: 259 VLGIFFYVGAEVSIGSFLVNYLSMPTIGGFTEQQATHYVSAYWTMAMIGRFAGSALLTRY 318 Query: 312 PAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALRDLGPHTSQ 371 +LA A + LL+ M +SG VA+++++ +GLFNSIMFPTIF+L + LGP T++ Sbjct: 319 SPRHMLALFAGINVLLLGTTMASSGQVALYSVVAIGLFNSIMFPTIFALGIERLGPLTNK 378 Query: 372 GSGILCLAIVGGAIVPLLQGVLADNLGIQLAFILPVVCYGFILFYGAKGSKM 423 S +L +AIVGGA+VP LQGVLAD++G+Q +FILP++CYG+++F+G G+++ Sbjct: 379 ASSLLIMAIVGGALVPYLQGVLADHIGLQPSFILPLLCYGYVIFFGLVGARL 430 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: 576 Number of extensions: 19 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: 438 Length adjustment: 32 Effective length of query: 391 Effective length of database: 406 Effective search space: 158746 Effective search space used: 158746 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 Apr 09 2024. 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