Align Low-affinity (212 (characterized)
to candidate BWI76_RS26235 BWI76_RS26235 gluconate transporter
Query= TCDB::P0AC96 (446 letters) >FitnessBrowser__Koxy:BWI76_RS26235 Length = 446 Score = 843 bits (2179), Expect = 0.0 Identities = 431/446 (96%), Positives = 443/446 (99%) Query: 1 MTTLTLVLTAVGSVLLLLFLVMKARMHAFLALMVVSMGAGLFSGMPLDKIAATMEKGMGG 60 M+TLTLVLTAVGSVLLLLFLVMKARMHAF+ALMVVS+GAGLFSGMPLDKIAATMEKGMGG Sbjct: 1 MSTLTLVLTAVGSVLLLLFLVMKARMHAFVALMVVSIGAGLFSGMPLDKIAATMEKGMGG 60 Query: 61 TLGFLAVVVALGAMFGKILHETGAVDQIAVKMLKSFGHSRAHYAIGLAGLVCALPLFFEV 120 TLGFLA+VVALGAMFGKILHETGAVDQIAVKMLKSFGHSRAHYAIGLAGL+CALPLFFEV Sbjct: 61 TLGFLAIVVALGAMFGKILHETGAVDQIAVKMLKSFGHSRAHYAIGLAGLICALPLFFEV 120 Query: 121 AIVLLISVAFSMARHTGTNLVKLVIPLFAGVAAAAAFLVPGPAPMLLASQMNADFGWMIL 180 AIVLLISVAFSMARHTGTNLVKLVIPLFAGVAAAAAFL+PGPAPMLLASQM+ADFGWMIL Sbjct: 121 AIVLLISVAFSMARHTGTNLVKLVIPLFAGVAAAAAFLLPGPAPMLLASQMHADFGWMIL 180 Query: 181 IGLCAAIPGMIIAGPLWGNFISRYVELHIPDDISEPHLGEGKMPSFGFSLSLILLPLVLV 240 IGLCAAIPGMIIAGPLWGNFISRYVELH PDDISEPHLGEGKMPSFGFSL+LILLPLVLV Sbjct: 181 IGLCAAIPGMIIAGPLWGNFISRYVELHTPDDISEPHLGEGKMPSFGFSLALILLPLVLV 240 Query: 241 GLKTIAARFVPEGSTAYEWFEFIGHPFTAILVACLVAIYGLAMRQGMPKDKVMEICGHAL 300 GLKTIAARFVPEGSTAYEWFEFIGHPFTAILVACLVAIYGLA+RQGM KD+VMEICGHAL Sbjct: 241 GLKTIAARFVPEGSTAYEWFEFIGHPFTAILVACLVAIYGLAVRQGMAKDRVMEICGHAL 300 Query: 301 QPAGIILLVIGAGGVFKQVLVDSGVGPALGEALTGMGLPIAITCFVLAAAVRIIQGSATV 360 QPAGIILLVIGAGGVFKQVLVDSGVGPALGEALTGMGLPIAITCFVLAAAVRIIQGSATV Sbjct: 301 QPAGIILLVIGAGGVFKQVLVDSGVGPALGEALTGMGLPIAITCFVLAAAVRIIQGSATV 360 Query: 361 ACLTAVGLVMPVIEQLNYSGAQMAALSICIAGGSIVVSHVNDAGFWLFGKFTGATEAETL 420 ACLTAVGLVMPVIEQL+YSGAQMAALSICIAGGSIVVSHVNDAGFWLFGKFTGATEA+TL Sbjct: 361 ACLTAVGLVMPVIEQLHYSGAQMAALSICIAGGSIVVSHVNDAGFWLFGKFTGATEAQTL 420 Query: 421 KTWTMMETILGTVGAIVGMIAFQLLS 446 KTWTMMETILGTVGAIVGMIAF LLS Sbjct: 421 KTWTMMETILGTVGAIVGMIAFTLLS 446 Lambda K H 0.328 0.142 0.423 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: 831 Number of extensions: 30 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: 446 Length of database: 446 Length adjustment: 32 Effective length of query: 414 Effective length of database: 414 Effective search space: 171396 Effective search space used: 171396 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