Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF340 PS417_01730 histidine ABC transporter substrate-binding protein
Query= TCDB::Q9KKE3 (346 letters) >FitnessBrowser__WCS417:GFF340 Length = 321 Score = 345 bits (886), Expect = e-100 Identities = 166/340 (48%), Positives = 230/340 (67%), Gaps = 25/340 (7%) Query: 7 TMRLTFAAAGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYDCQV 66 T+ T +AG++ ASA A +C GK V FAG++WESG +T++++T+L KGYDC+ Sbjct: 6 TLMATLLSAGVL--ASAGAQAAGWCESGKPVKFAGLNWESGMLLTDILQTVLEKGYDCKT 63 Query: 67 DSIPGNSVTLEQATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFVGASEGWFVPD 126 DS+PGNS+T+E A ++ND+Q+FAEEW+GRS+VWNKA + KV+ VG VGA EGW+VP Sbjct: 64 DSLPGNSITMENALSSNDIQVFAEEWVGRSEVWNKAEKAGKVVGVGAPVVGAIEGWYVPR 123 Query: 127 YVVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGVSTAK 186 YV+ GD R +EAKAPDLK+++ L K A +F D EEPSKGRF NCP+GWTCE ++ Sbjct: 124 YVIEGDAKRKLEAKAPDLKNIADLA--KYASVFKDQEEPSKGRFYNCPAGWTCELDNSEM 181 Query: 187 LEAYKLGETYVNFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEE-PAY 245 L++Y L TY NFRPGTG ALDAA+ S+Y +GEPI FYYWSPT ++G+ L++LEE P Sbjct: 182 LKSYGLESTYTNFRPGTGPALDAAVLSSYKRGEPILFYYWSPTPLMGQVDLVKLEEKPGV 241 Query: 246 NEACWKELSSANGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNASLA 305 ++ SV + G++ TF +APE+V +LEK P+D +N +L Sbjct: 242 DK--------------------SVSIKVGLSKTFHEQAPELVAVLEKVNLPIDLLNQNLG 281 Query: 306 YMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGL 345 MA ++++ A FLK ++W WVSD+A KI+A L Sbjct: 282 RMAKERIESPKLAKIFLKEHPEVWHAWVSDDAAKKIDAAL 321 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: 329 Number of extensions: 15 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: 346 Length of database: 321 Length adjustment: 28 Effective length of query: 318 Effective length of database: 293 Effective search space: 93174 Effective search space used: 93174 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