Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Ga0059261_0628 Ga0059261_0628 L-threonine O-3-phosphate decarboxylase (EC 4.1.1.81)
Query= curated2:A5FVN2 (364 letters) >FitnessBrowser__Korea:Ga0059261_0628 Length = 319 Score = 87.0 bits (214), Expect = 6e-22 Identities = 100/296 (33%), Positives = 133/296 (44%), Gaps = 43/296 (14%) Query: 59 RYPDGGA-TSLRAAIGRRFCLDPARIVCGNGSDDLIALLIQSYGGPGTELVMSRHGFLIY 117 R PD A T L R F DPA ++ G++ + LL GG V R+G+ Y Sbjct: 49 RLPDASALTGLETTAARYFGADPACVLAVPGTEIGLRLL----GGHLPRPV--RYGWPSY 102 Query: 118 EIAARLAGMNVRKAPERNLTADIDAMLAEVTPATRLVFLANPNNPTGSLVPASDVSRLRA 177 G + AP+ D P + LANPNNP G + PA+ LRA Sbjct: 103 -------GTHAEIAPDGVAVDGPD-------PGAGTLILANPNNPDGRITPAA---ALRA 145 Query: 178 ELPPDVLLVLDAAYAEYVERADYDPGVELVDSGQNT---VMTRTFSKMFGLGGVRLGWAY 234 +L LVLD A+A D DP L + + ++ R+F K FGL GVRLG+ Sbjct: 146 QLAAG-WLVLDEAFA------DTDPRHSLAGAVREATPLIVLRSFGKFFGLAGVRLGFVI 198 Query: 235 APLAIVDVLNRTRMPFNVSGPAAAAGIAALAEPGWVERCRNHNTRARTELAA--RIERAG 292 AP ++ L R + VS A A G AA A+ GW+E R R + AA ++ RA Sbjct: 199 APPELIATLRRHLGSWPVSAAAIAIGTAAYADSGWIEAER---IRLAADAAALDQLLRAH 255 Query: 293 FRVWPSEANFLLADLETADRAAAADTHLRSRGIIVRQVAAYGLPQCLRITIGTDEE 348 + P A L +ETAD A A L R I+ R P+ LRI + D E Sbjct: 256 GHI-PIGACPLFRLIETAD-AQALFERLARRSILTRPFDYD--PRWLRIGLPADAE 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: 310 Number of extensions: 18 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: 319 Length adjustment: 28 Effective length of query: 336 Effective length of database: 291 Effective search space: 97776 Effective search space used: 97776 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