Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate Dsui_0540 Dsui_0540 L-threonine-O-3-phosphate decarboxylase
Query= curated2:Q67KI2 (361 letters) >FitnessBrowser__PS:Dsui_0540 Length = 334 Score = 83.2 bits (204), Expect = 9e-21 Identities = 81/247 (32%), Positives = 114/247 (46%), Gaps = 30/247 (12%) Query: 90 GSDEVFRLLAEVYLEPGDRVVVPEPSFAAYRFVAELMGAEVVAVPLAGWTMDLPAMAEAA 149 GS + L ++ L PG R V PS+A + A + AE P A P E Sbjct: 72 GSQAAIQTLPKL-LPPG-RAAVLAPSYAEH--AAAWVKAEWAVTPFA------PPRLEEV 121 Query: 150 ARGAKLLFLCRPNNPTGTVFAEADLRAALERVPP-STLVVVDEAYREFDETPFDSRALV- 207 A+ ++ + PNNPTG LRAA + L+VVDEA+ + D P DS A + Sbjct: 122 AKEHNVVVVVNPNNPTGERITARRLRAAARALAKRGGLLVVDEAFADAD--PRDSLADLA 179 Query: 208 --QDYPNVVIARTFSKIYGMAGFRLGYGVMRPEVLAPLYTARDPFSVNGLAVAAGLAALD 265 + PN+++ R+ K +G+AG R+G+ + RPE+L L P+ V G A AL+ Sbjct: 180 GTKAAPNIIVLRSLGKFFGLAGARVGFAIGRPELLEALADTLGPWPVAGPARWVARCALE 239 Query: 266 DVEHVERTRALTREGKAYLYAAFQRL------GLGYVPSEANFVLFDAGRPAAEVFDALL 319 D RA + + L A +RL LG F R A V+D L Sbjct: 240 D-------RAWQADMRQELQVAAERLETLLQDSLGASTGTGLFRWLPHPR-ADWVYDELA 291 Query: 320 RRGVLVR 326 RRG+LVR Sbjct: 292 RRGILVR 298 Lambda K H 0.322 0.138 0.408 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: 286 Number of extensions: 19 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: 361 Length of database: 334 Length adjustment: 29 Effective length of query: 332 Effective length of database: 305 Effective search space: 101260 Effective search space used: 101260 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 (21.9 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