Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate 15431 b1311 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= uniprot:C8WUR0 (321 letters) >FitnessBrowser__Keio:15431 Length = 293 Score = 116 bits (290), Expect = 8e-31 Identities = 86/279 (30%), Positives = 132/279 (47%), Gaps = 24/279 (8%) Query: 28 LSPALVTICVLSILPIFYTIYISFTNFNQMHFLSYQFVGLKNYEELLNPHDPLSNLFLPT 87 L+P+L+ + L P+ I ISF + FVG+ NY +L+ +L++ Sbjct: 18 LAPSLLLLGGLVAWPMVSNIEISFLRLPLNPNIESTFVGVSNYVRILSDPGFWHSLWMTV 77 Query: 88 FIWTLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYRTLLIVPWAVPNLISMLAWQGLL 147 + LV A +T L V +F N+ R R R+L+I+ + P++ + AW+ + Sbjct: 78 WYTALVVA-GSTVLGLAVAMFF-----NREFRLRKTARSLVILSYVTPSISLVFAWKYMF 131 Query: 148 NDQYGQINAL----LHGVFGLPRIPWLTSALWARIAVIMVNVWAGFPYMMTVCLGALQSI 203 N+ YG +N L LH P W + + + V++ +W FPY L LQ+I Sbjct: 132 NNGYGIVNYLGVDLLHLYEQAPL--WFDNPGSSFVLVVLFAIWRYFPYAFISFLAILQTI 189 Query: 204 PTDQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSYNFNNFNASYLLTGGGPPNS 263 YEAAE+DGAN WQ FR VT+P++ + ++ + F F YLLT Sbjct: 190 DKSLYEAAEMDGANAWQRFRIVTLPAIMPVLATVVTLRTIWMFYMFADVYLLT------- 242 Query: 264 NNPFLGQTDILATAAYKMTLTFNRYDLGATISVLLFILV 302 + DIL YK FN A ISV+LFI++ Sbjct: 243 -----TKVDILGVYLYKTAFAFNDLGKAAAISVVLFIII 276 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: 282 Number of extensions: 16 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: 293 Length adjustment: 27 Effective length of query: 294 Effective length of database: 266 Effective search space: 78204 Effective search space used: 78204 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: 48 (23.1 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