Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate HSERO_RS11490 HSERO_RS11490 ABC transporter permease
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__HerbieS:HSERO_RS11490 Length = 328 Score = 208 bits (529), Expect = 2e-58 Identities = 122/336 (36%), Positives = 184/336 (54%), Gaps = 16/336 (4%) Query: 9 TSASTTMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQ 68 TS+ST A+ +A + + L A+LL M + F+F S NF+ +++ Sbjct: 3 TSSSTPAASRQAA-------YLAGFKNYLGLMAALLAMCVMFAFLSENFLSAATFITLSN 55 Query: 69 STAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGAL 128 V+++ T+++I GIDLSVG++M A M + + WG PL + AL Sbjct: 56 DIPPLVVMSVGMTFILIIGGIDLSVGSVMALAASMLSMAMVRWGWPLYAAAPLGVVVAAL 115 Query: 129 SGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGDL 188 G ++GMV ++P FI +LG++ + +GL+ ++ +R Y I+ L G Sbjct: 116 CGTLTGMVSVHWRIPSFIVSLGVLEIARGLAYQVTNSRTEYIGSA--VDVISSPILFG-- 171 Query: 189 IPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTF 248 + A L + I A ++L +TV GRY +G+NEEA+RLSGV + K+ + Sbjct: 172 -----MSPAFLSAIAIVIIAQLVLTRTVLGRYWIGIGTNEEAVRLSGVNPNPSKILAFAL 226 Query: 249 SGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMS 308 GA+ GIA L SRL +A P G G EL IAAVVIGGTSL GG G+I+ T IG I+S Sbjct: 227 MGALAGIAALFQVSRLEAADPNGGVGMELQVIAAVVIGGTSLMGGRGSIVSTFIGVLIIS 286 Query: 309 VLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRR 344 VL GL + V++ + ++TG +I++AV LD RRR Sbjct: 287 VLEAGLAQVGVSEPMKRIITGAVIVVAVILDTYRRR 322 Lambda K H 0.326 0.139 0.398 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: 229 Number of extensions: 11 Number of successful extensions: 3 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: 347 Length of database: 328 Length adjustment: 28 Effective length of query: 319 Effective length of database: 300 Effective search space: 95700 Effective search space used: 95700 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: 49 (23.5 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