Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate BPHYT_RS35660 BPHYT_RS35660 membrane protein
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS35660 Length = 283 Score = 135 bits (339), Expect = 1e-36 Identities = 85/270 (31%), Positives = 139/270 (51%), Gaps = 14/270 (5%) Query: 19 LAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAFIASLL 78 L VV+L P A +L ++ PA+++ P W P S + + A A F +L Sbjct: 20 LVVVVLFPFAVMLFTALKPASEIFVYPARWLPVHWQWSNFSDMWVA------ANFGVALR 73 Query: 79 NSIKVAGMATLAAVVVAVPAAWAVSRTPAVAWSLYA--VIATYMLPPVALAVPLYMGLAY 136 NS ++ ++T A+ V++PAA+A++R P LY ++ T ML P+ L V L+ A Sbjct: 74 NSTVISLLSTALALAVSLPAAYALARFPFRGRGLYRQFLLVTQMLSPILLVVGLFRLAAM 133 Query: 137 F-----GLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARLDQILRIL 191 L++S G+ + Y F W+L S F ++PR++E +A ++G + + + Sbjct: 134 IPYGDGNLVDSKIGVIVSYAAFNIAFAVWMLSSYFQTVPRDLEESAWLEGCGRTKAVFKV 193 Query: 192 TLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGR-VSDYGLIAT 250 LPLA P + +A+F F+ AW+EF KTLTV + D+ G+ V + L+ Sbjct: 194 FLPLAVPAIVVTAIFTFINAWNEFAVVYTLIRSPENKTLTVQVTDMVAGKYVVQWHLVMA 253 Query: 251 AGVLAALPPVLIGLIMQRALISGLTSGGVK 280 A + A LP ++ +QR L+ GL G VK Sbjct: 254 ATLCATLPVSVVFAWLQRYLVKGLALGAVK 283 Lambda K H 0.325 0.136 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: 205 Number of extensions: 13 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: 281 Length of database: 283 Length adjustment: 26 Effective length of query: 255 Effective length of database: 257 Effective search space: 65535 Effective search space used: 65535 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 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 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