Align Rhizopine-binding protein (characterized, see rationale)
to candidate Pf1N1B4_4386 Inositol transport system sugar-binding protein
Query= uniprot:A0A0N9WNI6 (308 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4386 Length = 308 Score = 354 bits (908), Expect = e-102 Identities = 177/298 (59%), Positives = 227/298 (76%), Gaps = 2/298 (0%) Query: 11 ALSLMLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQFEDARSDVVK 70 A L L S A A RIGVS+++ DD ++TY+R ++ A+ + V++QFEDA+ DVV+ Sbjct: 9 ATLLFLFSQWAAASYRIGVSIARVDDNFMTYVRSGLEDAARK--ENVQIQFEDAQGDVVR 66 Query: 71 QLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLKLPKGVITVA 130 QL+QV+ F+ QKVDA++V PVDTAAT +T AAV+A IPLVYVNR PD+ LPKGV+TVA Sbjct: 67 QLNQVQGFLGQKVDAVIVLPVDTAATANMTRAAVEAKIPLVYVNRHPDERVLPKGVVTVA 126 Query: 131 SNDLEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEVLAKYPGIKIDQEQT 190 SND+EAGQ+QM+YLAEKM GKG+I I+ GDLA NST +RT+GV +VL YPGIKI ++Q+ Sbjct: 127 SNDVEAGQLQMRYLAEKMAGKGNIAIIKGDLAQNSTQDRTEGVNQVLKDYPGIKIVEQQS 186 Query: 191 GTWSRDKGMTLVNDWLTQGRKFDAIVSNNDEMAIGAAMALKQAGVEKGSVLIAGVDGTPD 250 W R+KGM L ++WL G FDAIV+NNDEMAIGAAMAL+QAG KG + I G+DG PD Sbjct: 187 AEWQRNKGMDLTSNWLLAGADFDAIVANNDEMAIGAAMALQQAGKAKGEIAIVGIDGLPD 246 Query: 251 GLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAKNEPVEQAVWVPYRLITPENVDQFK 308 GL A+K+G L SVFQD QA ++ AA+KM K EPVE VWVP++LITP+ V F+ Sbjct: 247 GLAAIKRGMLVASVFQDPKAQATSALQAAIKMIKGEPVETDVWVPFQLITPDQVAVFE 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: 318 Number of extensions: 7 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: 308 Length of database: 308 Length adjustment: 27 Effective length of query: 281 Effective length of database: 281 Effective search space: 78961 Effective search space used: 78961 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