Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate BWI76_RS03245 BWI76_RS03245 maltodextrin ABC transporter permease
Query= uniprot:C8WUR0 (321 letters) >FitnessBrowser__Koxy:BWI76_RS03245 Length = 427 Score = 202 bits (515), Expect = 9e-57 Identities = 110/295 (37%), Positives = 175/295 (59%), Gaps = 7/295 (2%) Query: 28 LSPALVTICVLSILPIFYTIYISFTNFNQMHFLS----YQFVGLKNYEELLNPHDPLSNL 83 L+PA + I+P+ T+ +S TN++ H + +VGLKN+ L S Sbjct: 132 LAPAFIACIAFIIMPMIITVLVSLTNYSAPHHIPPKNLVDWVGLKNFITLFELRI-WSKT 190 Query: 84 FLPTFIWTLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYRTLLIVPWAVPNLISMLAW 143 F+ +WT+++A T G LA+ L NK + + +R + I+P+A+P +++L + Sbjct: 191 FVGIGVWTVLWAFFATLCTCSFGFLLALALENKKIIAKKAWRVVFILPYAIPAFVTLLIF 250 Query: 144 QGLLNDQYGQINALLHGVFGLPRIPWLTSALWARIAVIMVNVWAGFPYMMTVCLGALQSI 203 + LLN G +N+ L+ +G+ I +L+ L A++ VI V+VW G PY M + GA+ +I Sbjct: 251 RLLLNG-IGPVNSTLNS-WGIDSIGFLSDPLIAKMTVIAVSVWVGAPYFMLLITGAMTNI 308 Query: 204 PTDQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSYNFNNFNASYLLTGGGPPNS 263 P D YEA+E+DGA+ +Q FR +T+P V P L+ +F++NFNNF A YLLT GGP N Sbjct: 309 PRDLYEASEVDGASKFQQFREITLPMVLHQVAPSLVMTFAHNFNNFGAIYLLTEGGPINP 368 Query: 264 NNPFLGQTDILATAAYKMTLTFNRYDLGATISVLLFILVALISWVQMRYTGAFKE 318 F G TDIL T YK+TL F +Y + + IS+++F+ +++ + Q R +FKE Sbjct: 369 EYRFAGHTDILITWIYKLTLDFQQYQIASVISIIIFLFLSIFAIWQFRRMKSFKE 423 Lambda K H 0.327 0.140 0.451 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: 410 Number of extensions: 19 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: 321 Length of database: 427 Length adjustment: 30 Effective length of query: 291 Effective length of database: 397 Effective search space: 115527 Effective search space used: 115527 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