Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate N515DRAFT_1879 N515DRAFT_1879 L-threonine O-3-phosphate decarboxylase
Query= curated2:Q46Y48 (376 letters) >FitnessBrowser__Dyella79:N515DRAFT_1879 Length = 336 Score = 73.9 bits (180), Expect = 6e-18 Identities = 73/230 (31%), Positives = 104/230 (45%), Gaps = 19/230 (8%) Query: 151 GHDLDAMAA-AITSDTR---LVFIANPNNPTGTFVPAAALETFLAKVPAEVV-VVLDEAY 205 GH ++ AA A+ S ++ + +PNNP G AL A + +V+DEA+ Sbjct: 107 GHKVERAAADALFSRAARYDVIVLIHPNNPGGERFELDALLALHASLARRGGWLVVDEAF 166 Query: 206 NEYLDDDQQYDSVAWVRRYPNLLVSRTFSKAYGLAGLRIGYAVAQPELTDLLNRIRQPFN 265 D DS+ P L+V R+ K +GLAG R G+ A+P L L P+ Sbjct: 167 I----DATPGDSLCEAHALPGLIVLRSVGKFFGLAGARAGFVCAEPALLVALRERLGPWT 222 Query: 266 VNSVAQAAAVAALGDTAFLQRSAELNRAGKAQLVEAFSRLGLEFVASSGNFVLVRVGDDD 325 ++ + AL DTA+ E A A+L +R GL A F R D Sbjct: 223 LSGPTRQVLKLALADTAWQAAQRERLHATSARLSALLARHGLAPAAGCAFFQWRR----D 278 Query: 326 DAGARVNVALLRQGVIVRPVGNYGMPRWLRVTIGLPDENAAFIAALERAL 375 + + AL RQGV+VR + P +R GLP + AAF A L+ AL Sbjct: 279 ERATAMQRALARQGVLVR---RFEQPHSIR--FGLPGDEAAF-ARLDAAL 322 Lambda K H 0.318 0.134 0.382 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: 327 Number of extensions: 17 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: 376 Length of database: 336 Length adjustment: 29 Effective length of query: 347 Effective length of database: 307 Effective search space: 106529 Effective search space used: 106529 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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