Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate HSERO_RS02200 HSERO_RS02200 mannitol ABC transporter permease
Query= uniprot:D8IPH9 (270 letters) >FitnessBrowser__HerbieS:HSERO_RS02200 Length = 271 Score = 124 bits (310), Expect = 3e-33 Identities = 75/249 (30%), Positives = 128/249 (51%), Gaps = 4/249 (1%) Query: 13 VGIVLVLVAVFPLLWALLNSVKTLLDIVTPTPRFLFTPTLENYRQVIGSPEVLVGLTNSA 72 +G +V FP+ W + + KT TP+ +F PTLE +R+V L + NS Sbjct: 14 LGWACAIVLFFPIFWVAVTAFKTESQAYTPS--LVFLPTLETFREVFSRSHYLGYVQNSL 71 Query: 73 VIVGSAVLLGTFMGVPAAYVIARYHVPGKRDIQFFLLSLRFLPPVAVAIPLIAIWVDLGL 132 ++ + LL + VPAAY +A + + + ++LS + +P V V IP+ + + GL Sbjct: 72 IVSLGSTLLSLLLAVPAAYSMAFFPTGRTQKLLLWMLSTKMMPAVGVLIPIYLMAKNTGL 131 Query: 133 YDTRFSMIVTYLLTTLSTITWLSIPVFQRMPREIEEAATLDGYGPYAVFWKIALPNCATT 192 DT + + Y L L W++ F +P+EI EAA +DG + + LP Sbjct: 132 LDTVTGLTIIYTLINLPIAVWMAFTYFNDVPKEILEAARIDGANAWQEMIYLLLPTAMPG 191 Query: 193 LLGGIIFSFVLVWNELMIALALTSSNSATLPVVASAFTSMGQEVPWGVINASTVLLALPP 252 L + +L WNE +L LTS N+A L V +++ S + + W ++A++ LLA+ P Sbjct: 192 LASTALLLVILSWNEAFWSLNLTSVNAAPLTVFIASY-SNPEGLFWAKLSAAS-LLAIAP 249 Query: 253 LIFVGVLSR 261 ++ +G L++ Sbjct: 250 IMALGWLAQ 258 Lambda K H 0.327 0.142 0.434 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: 200 Number of extensions: 14 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: 270 Length of database: 271 Length adjustment: 25 Effective length of query: 245 Effective length of database: 246 Effective search space: 60270 Effective search space used: 60270 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 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