Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate CA265_RS11675 CA265_RS11675 aspartate aminotransferase
Query= curated2:Q4FP52 (360 letters) >FitnessBrowser__Pedo557:CA265_RS11675 Length = 399 Score = 76.6 bits (187), Expect = 1e-18 Identities = 64/210 (30%), Positives = 100/210 (47%), Gaps = 12/210 (5%) Query: 78 ERIICGAGSDEIIQMICQLYLKPSDEVIVPQYSFLMYRIYA---QIVGAKVVFSKEKNFK 134 E I+ G E I + Q + DE+I+P+ + Y +A +V ++ E F Sbjct: 90 ENILVTVGGSEAITIAMQTCVNEGDEIIIPEPFYANYNGFACMSNVVVKPILSYIENGFA 149 Query: 135 VS-INEIIKKVTRKTKLVFIANPNNPTGTYLTRAELIDLRKKLNK-NILLVLDDAYFEY- 191 + I E K +T KTK + I NPNNPTG +RAEL L+ K ++ L D+AY E+ Sbjct: 150 LPPIAEFEKLITEKTKAIIICNPNNPTGYLYSRAELEALKTLCVKYDLFLFSDEAYREFC 209 Query: 192 MKNKDYKSGLDLFKNKDNVVVIRTFSKIYGLASLRVGWGHGPKKIISAMNL-----IRPP 246 +++ S + L +NVV++ T SK Y R+G K + A L P Sbjct: 210 YDGREFISPMHLDGLDENVVIMDTVSKRYSACGARLGCLITKNKEVIASGLKFAQARLSP 269 Query: 247 FNVNQVAQMAAIEALKDRKFINNSVKHNIR 276 V Q+A AA++ D F + ++ +R Sbjct: 270 GMVEQIAGAAAVDT-PDSYFEKVNTEYTLR 298 Lambda K H 0.321 0.137 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: 326 Number of extensions: 14 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: 399 Length adjustment: 30 Effective length of query: 330 Effective length of database: 369 Effective search space: 121770 Effective search space used: 121770 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: 50 (23.9 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