Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate PfGW456L13_3631 Histidine ABC transporter, histidine-binding protein (TC 3.A.1)
Query= TCDB::Q9KKE3 (346 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3631 Length = 316 Score = 309 bits (792), Expect = 5e-89 Identities = 151/328 (46%), Positives = 206/328 (62%), Gaps = 21/328 (6%) Query: 18 MLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGYDCQVDSIPGNSVTLE 77 +L SAS + +C GK+V FAG++WESG +T++M +L GY C D + GN++ LE Sbjct: 10 LLVGSASSQASGWCESGKSVKFAGLNWESGMLLTDIMMIVLKDGYGCTTDQLVGNTIILE 69 Query: 78 QATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFVGASEGWFVPDYVVHGDPARNI 137 A A ND+Q+F EEW+ RS+VW KAV KV+ VG +GA++GW+VP YVV GD RN Sbjct: 70 TALAGNDIQVFGEEWMERSEVWKKAVAAGKVVGVGAPIIGATQGWYVPRYVVEGDAKRNR 129 Query: 138 EAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGVSTAKLEAYKLGETYV 197 A+APDL++V+ L+ K A +F D EEPSKGRF NCP+GW CE +T L+ Y L T+ Sbjct: 130 PAQAPDLRTVADLS--KYASVFRDSEEPSKGRFYNCPAGWICEQDNTEMLKEYGLENTFT 187 Query: 198 NFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEEPAYNEACWKELSSAN 257 NFRPGTG ALDAA+ S+Y +GEP+ FYYWSPT ++G+ I+LEE + AN Sbjct: 188 NFRPGTGAALDAAVLSSYKRGEPVLFYYWSPTPLMGQIDAIRLEEK----------TGAN 237 Query: 258 GKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNASLAYMADNKVDATAA 317 V G++ F +APE+V +LEK P+D +N +LA M ++++ Sbjct: 238 ---------KDVITMVGLSKAFHEQAPELVAVLEKVNIPIDLLNQNLARMTRERIESPKL 288 Query: 318 AAEFLKTKGDIWSKWVSDEARGKIEAGL 345 A FLK +IW WV + A KIEA L Sbjct: 289 ARMFLKEHPEIWHAWVDEAAAKKIEASL 316 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: 310 Number of extensions: 12 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: 316 Length adjustment: 28 Effective length of query: 318 Effective length of database: 288 Effective search space: 91584 Effective search space used: 91584 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