Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate PfGW456L13_4239 L-threonine 3-O-phosphate decarboxylase (EC 4.1.1.81)
Query= curated2:Q1LT68 (360 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4239 Length = 330 Score = 72.8 bits (177), Expect = 1e-17 Identities = 49/132 (37%), Positives = 77/132 (58%), Gaps = 13/132 (9%) Query: 143 LDCVKLIYICHPNNPTGNIINPSDIRQLLDITHGRTI-----LVVDEAYIDFYPTASISS 197 +D ++ + +PNNPTG + PS +LLD H R LVVDEA++D P S++ Sbjct: 122 IDSFDVLVVVNPNNPTGLSLTPS---RLLD-WHTRLAQRGGWLVVDEAFMDNTPQLSLAP 177 Query: 198 WINHYPHLVILRTLSKAFALAGLRCGFILANPDIIKLLLKVIAPYPISRPVVDIAKQAL- 256 + H L++LR+ K F LAG+R GF+LA ++KLL + + P+ +S + + L Sbjct: 178 FA-HQVGLIVLRSFGKFFGLAGVRLGFVLAERKLLKLLAEQVGPWAVSGATRVVGQACLR 236 Query: 257 STKGIHQTKRRV 268 T+G QT++RV Sbjct: 237 DTEG--QTRQRV 246 Lambda K H 0.323 0.138 0.428 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: 257 Number of extensions: 15 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: 360 Length of database: 330 Length adjustment: 29 Effective length of query: 331 Effective length of database: 301 Effective search space: 99631 Effective search space used: 99631 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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