Align Inositol transport system sugar-binding protein (characterized)
to candidate BPHYT_RS01825 BPHYT_RS01825 sugar ABC transporter substrate-binding protein
Query= reanno::WCS417:GFF2331 (309 letters) >FitnessBrowser__BFirm:BPHYT_RS01825 Length = 339 Score = 131 bits (329), Expect = 3e-35 Identities = 88/293 (30%), Positives = 146/293 (49%), Gaps = 11/293 (3%) Query: 20 VASAADLKIGVSMSAFDDTFLTYLREDMDKQAKSYPKGDGVQLQFEDARADVVKQLSQVE 79 +AS LK+G + + ++ + R K K G QL DA + KQ+S ++ Sbjct: 45 LASKTPLKVGFAQTESNNPW----RLAETKSFKDIAAKCGWQLVMTDANSSNSKQVSDIQ 100 Query: 80 NFISQKVDAIIVNPVDTASTANIIKAATAAKIPLVFVNRRPDSQTLAPG---VAAVTSDD 136 N I+Q VD ++ P + A ++ A A IP++ V+R D G + + SD Sbjct: 101 NMIAQHVDLLVFPPREEKPLAPVVLQAKKAGIPVILVDRDVDQSVAKAGRDYITFIGSDF 160 Query: 137 VEAGKLQMQYIAEKLGGKGNIVILLGDLANNSTTNRTKGVKEVLTKYPGIKIEQEQTGIW 196 ++ G ++ + GGK I+ L G ++ +R KG E++ K PG+ I Q+G + Sbjct: 161 IDQGHRAADWLVKATGGKAKIIELEGTTGASAANDRKKGFDEIIAKNPGMTIIASQSGDF 220 Query: 197 LRDRGMTLVNDWLTQGRDFQAVLSNNDEMAIGAAMALKSAGK---KGVLIAGVDGTPDGL 253 RD+G ++ L D AV ++NDEMA+GA A+K+AGK K + I +DGT G+ Sbjct: 221 ARDKGRQVMETLLQAHPDVTAVYAHNDEMALGAIAAIKAAGKQPGKDIQIVTIDGTKGGM 280 Query: 254 NAITKGDMTVSAFQDAKGQADKSVETARKMAKNEPIEQNVVIPFQLITPDNVK 306 +AI G++ S Q + + + A++ AK E I V + + NV+ Sbjct: 281 DAIAAGELGASV-QSSPFFGPLACDVAQRYAKGEKIPTWVKVSDKFYDKSNVQ 332 Lambda K H 0.314 0.131 0.357 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: 239 Number of extensions: 12 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: 309 Length of database: 339 Length adjustment: 28 Effective length of query: 281 Effective length of database: 311 Effective search space: 87391 Effective search space used: 87391 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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