Align ABC transporter for D-Glucosamine, permease component 1 (characterized)
to candidate HSERO_RS02200 HSERO_RS02200 mannitol ABC transporter permease
Query= reanno::Smeli:SM_b21219 (281 letters) >FitnessBrowser__HerbieS:HSERO_RS02200 Length = 271 Score = 129 bits (325), Expect = 5e-35 Identities = 82/263 (31%), Positives = 144/263 (54%), Gaps = 12/263 (4%) Query: 20 AVVILAPVAWLLIMSISPAADLSAKPLAWWPSDIDLSRYRTLLSAVENSAGAAFIASLLN 79 A+V+ P+ W+ + + + L + P+ L +R + S + ++ + N Sbjct: 19 AIVLFFPIFWVAVTAFKTESQAYTPSLVFLPT---LETFREVFSR------SHYLGYVQN 69 Query: 80 SIKVAGMATLAAVVVAVPAAWAVSRTPAVAWS--LYAVIATYMLPPVALAVPLYMGLAYF 137 S+ V+ +TL ++++AVPAA++++ P L +++T M+P V + +P+Y+ Sbjct: 70 SLIVSLGSTLLSLLLAVPAAYSMAFFPTGRTQKLLLWMLSTKMMPAVGVLIPIYLMAKNT 129 Query: 138 GLLNSVFGLALVYLTILAPFTTWLLKSGFDSIPREIESAAMIDGARLDQILRILTLPLAA 197 GLL++V GL ++Y I P W+ + F+ +P+EI AA IDGA Q + L LP A Sbjct: 130 GLLDTVTGLTIIYTLINLPIAVWMAFTYFNDVPKEILEAARIDGANAWQEMIYLLLPTAM 189 Query: 198 PVMATSALFAFLLAWDEFFYALLFTSDQRAKTLTVAIADLAGGRVSDYGLIATAGVLAAL 257 P +A++AL +L+W+E F++L TS A LTV IA + + ++ A +LA Sbjct: 190 PGLASTALLLVILSWNEAFWSLNLTS-VNAAPLTVFIASYSNPEGLFWAKLSAASLLAIA 248 Query: 258 PPVLIGLIMQRALISGLTSGGVK 280 P + +G + Q+ L+ GLT G VK Sbjct: 249 PIMALGWLAQKQLVRGLTFGAVK 271 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: 202 Number of extensions: 11 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: 271 Length adjustment: 25 Effective length of query: 256 Effective length of database: 246 Effective search space: 62976 Effective search space used: 62976 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