Align Rhizopine-binding protein (characterized, see rationale)
to candidate Pf6N2E2_1015 Inositol transport system sugar-binding protein
Query= uniprot:A0A0N9WNI6 (308 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1015 Length = 307 Score = 323 bits (829), Expect = 2e-93 Identities = 164/297 (55%), Positives = 219/297 (73%), Gaps = 2/297 (0%) Query: 12 LSLMLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQFEDARSDVVKQ 71 L + L + ALAD+RIGVS++Q DD +L +R+ M AK +P GV LQFEDA+ DVV+Q Sbjct: 9 LFVALFAPLALADIRIGVSIAQVDDVFLAQMRDYMAAHAKDLP-GVNLQFEDAQGDVVRQ 67 Query: 72 LSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLKLPKGVITVAS 131 L+QV++F +Q +DAI+VNPVDTAAT+K+T A KA +PLVYVNRRPD +LP GV V S Sbjct: 68 LNQVQNFTAQGMDAIIVNPVDTAATQKMTAHAQKASVPLVYVNRRPDQAELPPGVGYVGS 127 Query: 132 NDLEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEVLAKYPGIKIDQEQTG 191 ++++AG+MQM+YLAEKM GKG++ I+LG L+NN+T NRT+GVKEVL YP I + +EQ+ Sbjct: 128 DEIKAGEMQMRYLAEKMGGKGNLAIMLGLLSNNATHNRTQGVKEVLKSYPDIHVVEEQSA 187 Query: 192 TWSRDKGMTLVNDWLTQGRKFDAIVSNNDEMAIGAAMALKQAGVEKG-SVLIAGVDGTPD 250 W R K M L+N+W+ G+K DA+ +N DEMAIGAAMA+ QAG+ G +L+ G DG P Sbjct: 188 EWQRSKAMDLMNNWILSGKKIDAVAANADEMAIGAAMAINQAGMRSGKDILVGGSDGGPA 247 Query: 251 GLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAKNEPVEQAVWVPYRLITPENVDQF 307 GL A+KK L V+V+QD GQA+ SID A+KM + EP + +PY+LIT N F Sbjct: 248 GLDAIKKDQLLVTVYQDNKGQAIGSIDLALKMIRKEPFAAELTIPYQLITKANYQDF 304 Lambda K H 0.315 0.130 0.360 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: 278 Number of extensions: 7 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: 308 Length of database: 307 Length adjustment: 27 Effective length of query: 281 Effective length of database: 280 Effective search space: 78680 Effective search space used: 78680 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: 41 (21.5 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