Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_068174047.1 HTA01S_RS17665 histidinol-phosphate aminotransferase family protein
Query= curated2:Q9RRM7 (361 letters) >NCBI__GCF_001592305.1:WP_068174047.1 Length = 360 Score = 335 bits (860), Expect = 9e-97 Identities = 176/356 (49%), Positives = 227/356 (63%), Gaps = 10/356 (2%) Query: 9 PGPSGVRQAVRDIPAYPFTPIDVPYKLDQNENPYDFPPELKQKAAERMLAHPWNRYPDLH 68 P P VR AV P YPF+PID P KLDQNE+ DFP LK A +RM PW+RY DLH Sbjct: 4 PLPPPVRAAVLASPDYPFSPIDAPVKLDQNESFADFPAPLKALALQRMQQLPWHRYTDLH 63 Query: 69 ADTLRAAIAGYEGWDAAGVVITPGSNVLIKILTELGGIGQTVLTTDPTFSVYTLEAAMLG 128 A+ L AAIA ++GW A+G V T GSNVLI +L +L +G VLT P F++Y L+A++LG Sbjct: 64 AEELTAAIARHDGWSASGTVATTGSNVLIALLVQLAALGGRVLTVKPNFALYALDASLLG 123 Query: 129 AELVLTPLNPDFSLPVEATLQALAAHAP--------GVFYVTQPHAPTGHSDRPEDVRRV 180 A L PL D SL ++A + AL A GV Y+ +PHAPTG +++ R+ Sbjct: 124 AALTEVPLRADHSLDMDALIAALGTDADTNAPAQPRGVIYLPRPHAPTGSLCELDELDRL 183 Query: 181 VEVADRLGWVTVIDEAYSQYAGTDYRELVRAGKHVLSLRTFSKAWGLAGVRAGYLLTNPE 240 GW+ VIDEAY + TD R L R HV+ LRTFSKAWGLAG+R GY L + E Sbjct: 184 ARACP--GWLLVIDEAYHHFTDTDARALARQHPHVVLLRTFSKAWGLAGLRLGYALASDE 241 Query: 241 LAGHLQKLVSAFTINFLTQAVIETALEHPEYMRERVAEAIAERGRIYAAVQGHPTCTIFP 300 +A L+KLV F ++ L ALEHP+Y+RERVA +ER R++ A+Q HPT + P Sbjct: 242 VARQLRKLVPPFGVSVLQTVSALVALEHPDYLRERVAHTRSERERLFKALQRHPTWQVAP 301 Query: 301 SNTNFFLLKTPDADAAYRHLLEHGIVCRRQDKLRGLDGCLRIAVGTPAENDALIAA 356 S+ NF L++TPDA A+ LL G++ RRQD L GL GCLR+ VG+ ENDA ++A Sbjct: 302 SHANFLLVRTPDAARAHAELLAQGVLVRRQDSLHGLQGCLRVTVGSVRENDAFLSA 357 Lambda K H 0.320 0.137 0.414 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: 394 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: 361 Length of database: 360 Length adjustment: 29 Effective length of query: 332 Effective length of database: 331 Effective search space: 109892 Effective search space used: 109892 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 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