Align Rhizopine-binding protein (characterized, see rationale)
to candidate WP_037153961.1 RHSP_RS23430 sugar ABC transporter substrate-binding protein
Query= uniprot:A0A0N9WNI6 (308 letters) >NCBI__GCF_000359745.1:WP_037153961.1 Length = 309 Score = 250 bits (639), Expect = 3e-71 Identities = 134/301 (44%), Positives = 197/301 (65%), Gaps = 6/301 (1%) Query: 11 ALSLMLASGAALADLRIGVSMSQFDDTWLTYLRESMDKQAKSMPDGVKLQFEDARSDVVK 70 AL+L+++S A AD RIGVSM + T + M AK+ G+ LQ DA +DV K Sbjct: 9 ALALVMSSQAYAAD-RIGVSMGYLTTNFQTLIANGMQDYAKTK--GLDLQVVDAANDVNK 65 Query: 71 QLSQVESFISQKVDAIVVNPVDTAATRKITEAAVKAGIPLVYVNRRPDDLK-LPKGVITV 129 QL QV +F + V AI+V+PVD+ T +++ A AGIPL+YVN +P DL L K V Sbjct: 66 QLDQVRNFAAGGVSAIIVDPVDSDGTPAMSKIAEDAGIPLIYVNIQPTDLSTLGKKQAFV 125 Query: 130 ASNDLEAGQMQMQYLAEKMKGKGDIVILLGDLANNSTTNRTKGVKEVL--AKYPGIKIDQ 187 SN+ E+G +Q + + + GKGD+V+++GDL++ + RT+ V +VL + GIK+ + Sbjct: 126 GSNETESGTLQTKEVCRMLGGKGDVVVMVGDLSSQAARQRTQDVHDVLKSSDCSGIKVVR 185 Query: 188 EQTGTWSRDKGMTLVNDWLTQGRKFDAIVSNNDEMAIGAAMALKQAGVEKGSVLIAGVDG 247 EQ G WSR G LV++WLT G F+A+++NNDEMA+GA A+K AG ++AG+D Sbjct: 186 EQVGNWSRVDGADLVSNWLTSGLTFNAVIANNDEMALGAISAIKNAGGSTDKTIVAGIDA 245 Query: 248 TPDGLRAVKKGDLAVSVFQDANGQAVDSIDAAVKMAKNEPVEQAVWVPYRLITPENVDQF 307 TPD L+A+K GDL V+VFQDA Q ++D AVK K E +++ VW+P++L+T +N+ QF Sbjct: 246 TPDALQAMKSGDLKVTVFQDAKAQGRGAVDTAVKAIKGEQIDREVWIPFKLVTKDNMVQF 305 Query: 308 K 308 + Sbjct: 306 E 306 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: 262 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 308 Length of database: 309 Length adjustment: 27 Effective length of query: 281 Effective length of database: 282 Effective search space: 79242 Effective search space used: 79242 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 24 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