Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate GFF81 PGA1_c00830 putative threonine-phosphate decarboxylase CobC
Query= curated2:A5FVN2 (364 letters) >FitnessBrowser__Phaeo:GFF81 Length = 356 Score = 57.4 bits (137), Expect = 6e-13 Identities = 51/175 (29%), Positives = 74/175 (42%), Gaps = 19/175 (10%) Query: 156 LANPNNPTGSLVPASDVSRLRAELPPDVLLVLDAAYAEYVERADYDPGVELVDSGQN--T 213 L +PNNP G A DV L+V+D ++ D P L+ Sbjct: 173 LVHPNNPDGRRWSAEDVQA--------PLVVIDESFC------DVCPADSLIHLANRPGV 218 Query: 214 VMTRTFSKMFGLGGVRLGWAYAPLAIVDVLNRTRMPFNVSGPAAAAGIAALAEPGWVERC 273 V+ ++F K +GL G+RLG+A +++ L + P+ VSGPA G AL + W E Sbjct: 219 VILKSFGKFWGLAGLRLGFAIGDPSLIGNLAAWQGPWAVSGPALRIGAQALRDADWAETT 278 Query: 274 RNHNTRARTELAARIERAGFRVWPSEANFLLADLETADRAAAADTHLRSRGIIVR 328 R + L + G ++ F L D+ D AAA L S I R Sbjct: 279 RARLQQDAKRLDKMVTGKGAKLVGGTDLFRLYDV---DDAAAWQARLASAQIWTR 330 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: 311 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: 356 Length adjustment: 29 Effective length of query: 335 Effective length of database: 327 Effective search space: 109545 Effective search space used: 109545 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