Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate AZOBR_RS10240 AZOBR_RS10240 L-threonine-O-3-phosphate decarboxylase
Query= curated2:A5FVN2 (364 letters) >FitnessBrowser__azobra:AZOBR_RS10240 Length = 339 Score = 80.1 bits (196), Expect = 8e-20 Identities = 79/266 (29%), Positives = 109/266 (40%), Gaps = 23/266 (8%) Query: 66 TSLRAAIGRRFCLDPARIVCGNGSDDLIALLIQSYGGPGTELVMSRHGFLIYEIAARLAG 125 T+LR A + + A V G + ++ PGT V+ G E AA A Sbjct: 63 TALREAAAACYGVPSADRVAAAGGSQALIQILPRLRRPGTVAVL---GPTYAEHAAGWAK 119 Query: 126 MNVRKAPERNLTA-DIDAMLAEVTPATRLVFLANPNNPTGSLVPASDVSRL-RAELPPDV 183 R A +L D D +V + NPNNP G +VP + L + Sbjct: 120 AGHRVAEVESLEGCDAD-----------VVVVVNPNNPDGRIVPPETLLALAERQAARGG 168 Query: 184 LLVLDAAYAEYVERADYDPGVELVDSGQNTVMTRTFSKMFGLGGVRLGWAYAPLAIVDVL 243 LV+D A+AE V V+ R+F K FGL GVRLG+ A+V L Sbjct: 169 WLVVDEAFAEVTPECS----VASEAGRAGLVILRSFGKFFGLAGVRLGFLLGEPALVRDL 224 Query: 244 NRTRMPFNVSGPAAAAGIAALAEPGWVERCRNHNTRARTELAARIERAGFRVWPSEANFL 303 P+ VSGPA AAL++ W+ R A AR+ AG RV + F Sbjct: 225 RAAVGPWAVSGPALTIATAALSDSAWIAATRRRLADAAARFDARLMEAGVRVAGGTSLFR 284 Query: 304 LADLETADRAAAADTHLRSRGIIVRQ 329 L D ++A L G++VR+ Sbjct: 285 LID---DPQSAGLYKELGLAGVLVRR 307 Lambda K H 0.320 0.136 0.405 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: 296 Number of extensions: 21 Number of successful extensions: 2 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: 364 Length of database: 339 Length adjustment: 29 Effective length of query: 335 Effective length of database: 310 Effective search space: 103850 Effective search space used: 103850 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