Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate BWI76_RS01820 BWI76_RS01820 maltose transporter permease
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__Koxy:BWI76_RS01820 Length = 296 Score = 105 bits (263), Expect = 9e-28 Identities = 84/284 (29%), Positives = 135/284 (47%), Gaps = 19/284 (6%) Query: 13 HASALLLAVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLS-AVENSAGA 71 H L+ I+ P+ ++ +S+ + + P I +R L +VE++ G Sbjct: 17 HLLLLVFIAAIMFPLLMVIAISLREGNFATGSLI---PESISWEHWRLALGFSVEHADGR 73 Query: 72 A------FIASLLNSIKVAGMATLAAVVVAVPAAWAVSRT--PAVAWSLYAVIATYMLPP 123 + L NSIKVAG+ + V ++ A+A +R P A L ++ M P Sbjct: 74 VTPPPFPVLLWLWNSIKVAGITAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPA 133 Query: 124 VALAVPLYMGLAYFGL------LNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAA 177 V V LY G LN+ G+ Y+ +A W +K F++I +E AA Sbjct: 134 VLSLVALYALFDRLGQYVPFVGLNTHGGVIFAYMGGIA-LHVWTIKGYFETIDGSLEEAA 192 Query: 178 MIDGARLDQILRILTLPLAAPVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADL 237 +DGA Q R++ LPL+ P++A + +F+ A E A L D + TL V + Sbjct: 193 ALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQY 252 Query: 238 AGGRVSDYGLIATAGVLAALPPVLIGLIMQRALISGLTSGGVKG 281 + +G A A VL+A+P ++ L+ QR L++GLT+GGVKG Sbjct: 253 LNPQNYLWGDFAAAAVLSAIPITVVFLLAQRWLVNGLTAGGVKG 296 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: 201 Number of extensions: 9 Number of successful extensions: 1 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: 296 Length adjustment: 26 Effective length of query: 255 Effective length of database: 270 Effective search space: 68850 Effective search space used: 68850 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: 48 (23.1 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