Align Histidinol-phosphate aminotransferase; Imidazole acetol-phosphate transaminase; HPAT; HspAT; EC 2.6.1.9 (characterized)
to candidate GFF3915 PS417_20045 threonine-phosphate decarboxylase
Query= SwissProt::P06986 (356 letters) >FitnessBrowser__WCS417:GFF3915 Length = 329 Score = 74.3 bits (181), Expect = 4e-18 Identities = 58/169 (34%), Positives = 86/169 (50%), Gaps = 17/169 (10%) Query: 83 GADEGIELLIRAFCEPGKDAILYCPPTYGMYSVSAETIGVECRTVPTLDNWQLDLQGISD 142 G+ I+LL R GK +L P Y ++ + G R V Q + Sbjct: 72 GSQAAIQLLPR-LRRAGKVGVL--SPCYAEHAEAWRRAGYVVREVQE--------QEVDF 120 Query: 143 KLDGVKVVYVCSPNNPTGQLINPQ---DFRTLLELTRGKAIVVADEAYIEFCPQASLAGW 199 L+G+ V+ V +PNNPTG + PQ D+ + L G +V DEA+++ PQ SLAG Sbjct: 121 FLEGLDVLVVVNPNNPTGLNLAPQRLLDWHSRLAQRGGWLVV--DEAFMDVTPQFSLAGH 178 Query: 200 LAEYPHLAILRTLSKAFALAGLRCGFTLANEEVINLLMKVIAPYPLSTP 248 A L +LR+ K F LAG+R GF LA +++ LL + + P+ +S P Sbjct: 179 -AHQVGLIVLRSFGKFFGLAGVRLGFVLAERKLLKLLAEQVGPWAVSGP 226 Lambda K H 0.319 0.135 0.396 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: 260 Number of extensions: 16 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: 356 Length of database: 329 Length adjustment: 29 Effective length of query: 327 Effective length of database: 300 Effective search space: 98100 Effective search space used: 98100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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