Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate BWI76_RS06700 BWI76_RS06700 putative maltodextrin transport permease
Query= uniprot:C8WUR0 (321 letters) >FitnessBrowser__Koxy:BWI76_RS06700 Length = 435 Score = 211 bits (538), Expect = 2e-59 Identities = 111/299 (37%), Positives = 172/299 (57%), Gaps = 5/299 (1%) Query: 25 YGYLSPALVTICVLSILPIFYTIYISFTNFNQMHFLSYQ---FVGLKNYEELLNPHDPLS 81 Y ++P + + + I PI + I+FTN+N H + +VG KN+ + S Sbjct: 137 YLMITPGFILLVFVVIFPILFGFAIAFTNYNLYHTPPAKLVDWVGFKNFINIFTLSIWRS 196 Query: 82 NLFLPTFIWTLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYRTLLIVPWAVPNLISML 141 F WT+V+ L T L VG+ LA+L+N K +R + + RT+ I+PWAVP +++L Sbjct: 197 TFF-DVLQWTVVWTLLATTLQCTVGVLLAILVNQKDLRFKPMIRTIFILPWAVPGFVTIL 255 Query: 142 AWQGLLNDQYGQINALLHGVFGLPRIPWLTSALWARIAVIMVNVWAGFPYMMTVCLGALQ 201 + G+ ND +G IN + FG+ WLT W + A+IM+ W GFP++ + G LQ Sbjct: 256 VFAGMFNDSFGVINNAILSFFGISPKAWLTDPFWTKTALIMMQTWLGFPFVFAMTTGVLQ 315 Query: 202 SIPTDQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSYNFNNFNASYLLTGGGPP 261 +IP D YEAA +DGA+ + R +T+P V P++I +++NFNNFN YL GGP Sbjct: 316 AIPDDLYEAATMDGASAFTRLRTITLPLVLYSIAPIIITQYTFNFNNFNIIYLFNNGGPA 375 Query: 262 NSNNPFLGQTDILATAAYKMTLTFNRYDLGATISVLLFILVALISWVQMRYTGAFKEVD 320 + + G TDIL + YK+T++ ++Y + ATI++LL I V ++ Q R T +FK D Sbjct: 376 VAGSN-AGGTDILVSWIYKLTMSSSQYAIAATITILLSIFVVGLALWQFRATKSFKNDD 433 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: 490 Number of extensions: 34 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: 321 Length of database: 435 Length adjustment: 30 Effective length of query: 291 Effective length of database: 405 Effective search space: 117855 Effective search space used: 117855 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: 50 (23.9 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