Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 1 (characterized)
to candidate WP_106712770.1 CU102_RS19475 carbohydrate ABC transporter permease
Query= reanno::WCS417:GFF2491 (276 letters) >NCBI__GCF_003010955.1:WP_106712770.1 Length = 289 Score = 201 bits (511), Expect = 2e-56 Identities = 111/280 (39%), Positives = 167/280 (59%), Gaps = 5/280 (1%) Query: 2 TLQQSRRLQSLLLGTLAWAIAILI-FFPIFWMVLTSFKTEIDAFATPPQFIFT-PTLENY 59 T ++SR L L L +A+++ FP++W+ SFK +ID FA PP+++ PTL++Y Sbjct: 9 THKRSRELFVRLSAYLTILVALVVTLFPVYWIAANSFKFDIDIFAVPPEWLPRHPTLKHY 68 Query: 60 LHINERSNYFSYAWNSVLISFSATALCLLISVPAAYSMA--FYETQRTKGTLLWMLSTKM 117 + + YA NS L++ T + + A Y++A Y Q K W+LST+M Sbjct: 69 DEAFIQRPFLRYALNSFLVAMGTTVVSVGFGTMAGYALARFSYPWQWRKQISFWILSTRM 128 Query: 118 LPPVGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLD 177 +PP+ ++P+YL F +L+T+ ALII YT NLP WM+ +YF+D+P ++ EAA +D Sbjct: 129 MPPIVSIIPLYLFFNYFDMLNTKSALIIAYTAFNLPFATWMMKSYFQDLPVELEEAAIVD 188 Query: 178 GATLWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLT-SSSAAPLTALIASYSSP 236 G T W + V LP+A+ GLA+T + LI+ WNE SL +T + + L IA + Sbjct: 189 GDTRWGAFLHVALPLARPGLAATAIFCLIISWNEFLLSLIITLTEQSQTLPIGIAGRVTQ 248 Query: 237 EGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276 +W ++SA +AC PI+IF +I QK LVRGLS GAVK Sbjct: 249 YKTYWGEISAAGFMACVPIVIFAFIVQKHLVRGLSLGAVK 288 Lambda K H 0.327 0.138 0.427 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: 266 Number of extensions: 14 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: 276 Length of database: 289 Length adjustment: 26 Effective length of query: 250 Effective length of database: 263 Effective search space: 65750 Effective search space used: 65750 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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