Align The Aldohexuronate (glucuronate, galacturonate) uptake porter (characterized)
to candidate GFF2889 PS417_14775 major facilitator transporter
Query= TCDB::P94774 (345 letters) >FitnessBrowser__WCS417:GFF2889 Length = 467 Score = 168 bits (426), Expect = 2e-46 Identities = 98/308 (31%), Positives = 148/308 (48%), Gaps = 25/308 (8%) Query: 8 RWYMIGLVTIGTVLGYLTRNAIAAAAPTLQEQLHISTQQYSYIIAAYSACYTIMQPVAGY 67 RW + ++ T + YL R ++ AP L Q S Y+ I A + Y I AG Sbjct: 20 RWTICAMLFFATTVNYLDRQVLSLLAPQLSTQFGWSNTDYANIAAVFQFVYAISMLFAGR 79 Query: 68 VLDVLGTKVGYAMFAILWALFCAGTALANSWG-GLAVARGAVGMA--------------- 111 +D +GTK Y + +W+ A + G G+A GA+G+A Sbjct: 80 FVDKIGTKAAYVVAIAIWSTGAIMHAFSVPMGEGIAAISGAIGLAVIPVSIAGFMLSRAV 139 Query: 112 ----EAAMIPAGLKASSEWFPAKERSVAVGYFNVGSSIGGMLAPPLVVWAIMAHSWQMAF 167 EA P +KA++E+FP KERS+A G FN G+++G +LAP V W+ AF Sbjct: 140 LAIGEAGNFPIAIKATAEYFPKKERSLATGIFNSGANVGAILAPICVPLIAGLWGWEAAF 199 Query: 168 LITGALSLVWALCWLYFYKHPKDQKKLSTEEREYILSGQEAQ----HQAGNAKRMSAW-Q 222 ++ G L VW + W+ Y+ P++QK+LS EE YI S Q Q AG ++ +W + Sbjct: 200 IVIGGLGFVWVVVWIALYQKPEEQKRLSPEELAYIRSDQTVQPFTPAPAGAPEKKVSWFK 259 Query: 223 ILRNRQFWGIALPRFLAEPAWGTFNAWIPLFMFKAYGFNLKEIAMFAWMPMLFADLGCIL 282 +L RQ W A +F+ + W F W+P ++ YG +I M + +G I Sbjct: 260 LLTYRQTWAFAFGKFMTDGVWWFFLFWLPTYLSAQYGMKGADIVMPLAVLYSMTMVGSIG 319 Query: 283 GGYMPMLF 290 GG+ P F Sbjct: 320 GGWFPSYF 327 Lambda K H 0.327 0.138 0.449 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: 590 Number of extensions: 33 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 345 Length of database: 467 Length adjustment: 31 Effective length of query: 314 Effective length of database: 436 Effective search space: 136904 Effective search space used: 136904 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