Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_011610725.1 TERY_RS04430 pyridoxal phosphate-dependent aminotransferase
Query= curated2:Q5P791 (356 letters) >NCBI__GCF_000014265.1:WP_011610725.1 Length = 390 Score = 68.6 bits (166), Expect = 3e-16 Identities = 88/294 (29%), Positives = 130/294 (44%), Gaps = 33/294 (11%) Query: 38 PSPR-ALAAIRAEASDA----LRLYPDPHADRLKAA--IATRFGVE---PREVFVGNGSD 87 P+PR AL AI D+ L+ A R A + +F + EV GS Sbjct: 43 PAPRHALEAISQSLQDSNTHGYSLFSSTQAFREAVARWYSNKFDISLNPETEVLALIGSQ 102 Query: 88 EVLAHAFMALLKHERPLRFPDISYSFYPVYCG---LYGIAFETVPL--DDDFAIRPDDYL 142 E AH +A+L P F + YP + G L G +PL ++ F D Sbjct: 103 EGTAHLPLAILD---PGDFALLQDPGYPSHSGGVYLAGGQVYPMPLLAENKFLPVLGDIP 159 Query: 143 PHGSVAAGGIIFPNPNAPTGRLMPLSDIERIVA--GNPQCVVVIDEAYVDF--GGESAIP 198 H A +I P+ PT + P+S ++ VA V+V D Y+DF S P Sbjct: 160 QHVLAQAKMMILSYPHNPTTAIAPISFLQEAVAFCQKHNLVLVHDAPYLDFVFNSSSEAP 219 Query: 199 LVRHHPNLLVVQ----TLSKSRSLAGLRVGFAVGNPDLIEALDRVKD--SFNSYPLDRLA 252 + V T+SKS S+ G RVG+A+GN LI+AL +VK FN Y R Sbjct: 220 SIFQADVEKSVSIEFFTMSKSYSMGGFRVGYAIGNAQLIQALRQVKACIDFNQY---RGI 276 Query: 253 IAGGVAAIEDEEHFQRTRMAVIATRERLSAD-LASLGFDV-LPSAANFVFTRHP 304 G +AA+ + R + + R + + L ++G+ V +PSA +V+T+ P Sbjct: 277 FNGAIAALTGPQEVVRKTVDIFRQRRDIFIEALDNIGWTVPMPSATMYVWTKLP 330 Lambda K H 0.323 0.140 0.417 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: 337 Number of extensions: 13 Number of successful extensions: 1 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: 356 Length of database: 390 Length adjustment: 30 Effective length of query: 326 Effective length of database: 360 Effective search space: 117360 Effective search space used: 117360 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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