Align Inositol transport system sugar-binding protein (characterized)
to candidate BWI76_RS07235 BWI76_RS07235 hypothetical protein
Query= reanno::WCS417:GFF2331 (309 letters) >FitnessBrowser__Koxy:BWI76_RS07235 Length = 307 Score = 291 bits (744), Expect = 2e-83 Identities = 156/298 (52%), Positives = 204/298 (68%), Gaps = 6/298 (2%) Query: 11 ALSMLLASGVASAADLKIGVSMSAFDDTFLTYLREDMDKQAKSYPKGDGVQLQFEDARAD 70 +L + V A D+ +GVSM+ FDD FLT LR M K+ + DGV+ Q EDA+ D Sbjct: 10 SLIACMLPAVVMAKDISVGVSMALFDDNFLTILRTAMQKEMQK----DGVKAQVEDAKGD 65 Query: 71 VVKQLSQVENFISQKVDAIIVNPVDTASTANIIKAATAAKIPLVFVNRRPDSQTLAPGVA 130 V +QL QV+NFI Q VDAIIVNPVDT + I+ AT A IPL+FVNRRP +Q L +A Sbjct: 66 VSQQLQQVQNFIGQGVDAIIVNPVDTNAVKPIMDQATKAGIPLIFVNRRPQAQ-LTDKMA 124 Query: 131 AVTSDDVEAGKLQMQYIAEKLGGKGNIVILLGDLANNSTTNRTKGVKEVLTKYPGIKIEQ 190 V SD V AG+LQM+ +A+ + GKGN+ ILLGDLAN ST +RTKGV+EV+ KYP IKI Q Sbjct: 125 YVGSDSVLAGRLQMEALAKAMNGKGNVAILLGDLANESTRDRTKGVEEVVAKYPDIKIVQ 184 Query: 191 EQTGIWLRDRGMTLVNDWLTQGRDFQAVLSNNDEMAIGAAMALKSAGKKGVLIAGVDGTP 250 +QT + R+ + +V++W+T G D QA+ SNNDEMAIGA AL +LIAGVDGTP Sbjct: 185 KQTAKFTRNDAVDVVSNWMTSGEDIQAIASNNDEMAIGALQAL-GKNPNHILIAGVDGTP 243 Query: 251 DGLNAITKGDMTVSAFQDAKGQADKSVETARKMAKNEPIEQNVVIPFQLITPDNVKDF 308 D L + G M + FQDAKGQ + +V+ A K+A E +E+ + +P+QLIT DN+ +F Sbjct: 244 DALQMLKNGKMIATIFQDAKGQGEGAVDAAIKLANGEKVEKVIDVPYQLITKDNMAEF 301 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: 274 Number of extensions: 9 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: 309 Length of database: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 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