Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate SMc00672 SMc00672 histidine-binding periplasmic signal peptide protein
Query= TCDB::Q9KKE3 (346 letters) >FitnessBrowser__Smeli:SMc00672 Length = 344 Score = 692 bits (1787), Expect = 0.0 Identities = 343/344 (99%), Positives = 343/344 (99%) Query: 3 MSISTMRLTFAAAGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGY 62 MSISTMRLTFAAAGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGY Sbjct: 1 MSISTMRLTFAAAGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGY 60 Query: 63 DCQVDSIPGNSVTLEQATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFVGASEGW 122 DCQVDSIPGNSVTLEQATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFVGASEGW Sbjct: 61 DCQVDSIPGNSVTLEQATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFVGASEGW 120 Query: 123 FVPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGV 182 FVPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGV Sbjct: 121 FVPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGV 180 Query: 183 STAKLEAYKLGETYVNFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEE 242 STAKLEAYKLGETYVNFRPGTGTALDAAITSAYLQGEPI FYYWSPTAILGKFKLIQLEE Sbjct: 181 STAKLEAYKLGETYVNFRPGTGTALDAAITSAYLQGEPILFYYWSPTAILGKFKLIQLEE 240 Query: 243 PAYNEACWKELSSANGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNA 302 PAYNEACWKELSSANGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNA Sbjct: 241 PAYNEACWKELSSANGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNA 300 Query: 303 SLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGLK 346 SLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGLK Sbjct: 301 SLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGLK 344 Lambda K H 0.314 0.130 0.391 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: 561 Number of extensions: 7 Number of successful extensions: 1 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: 346 Length of database: 344 Length adjustment: 29 Effective length of query: 317 Effective length of database: 315 Effective search space: 99855 Effective search space used: 99855 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: 49 (23.5 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