Align Histidinol-phosphate aminotransferase; EC 2.6.1.9 (characterized, see rationale)
to candidate WP_013721469.1 ALIDE2_RS04145 histidinol-phosphate transaminase
Query= uniprot:A0A2R7PAQ8 (373 letters) >NCBI__GCF_000204645.1:WP_013721469.1 Length = 372 Score = 533 bits (1374), Expect = e-156 Identities = 275/371 (74%), Positives = 304/371 (81%) Query: 3 TPASSPLQALARIRPDVRAMHSYVVQPSTGMLKMDAMENPFRLPAHLQAALGQRLGSVAL 62 T A+ AL RIR DVRAMH+Y V +TG LKMDAMENPF LP LQAALGQRLG +AL Sbjct: 2 TDATPQSLALQRIRADVRAMHAYAVHDATGYLKMDAMENPFGLPPALQAALGQRLGQLAL 61 Query: 63 NRYPGDRIADLKAALAQYAGMPEGYGIVLGNGSDELITLLALACAQPGTGQRATMLAPMP 122 NRYPG R DLKAALA +A PEG ++LGNGSDELI L+ LACA+ A +LAP P Sbjct: 62 NRYPGTRQNDLKAALAAHALAPEGSALILGNGSDELIGLVQLACARRDASGPAKVLAPAP 121 Query: 123 GFVMYPLSAQLQGLDFVGVPLTPDFELDEPAMLAAIGQHRPAITYIAYPNNPTATLWDEG 182 GFVMY + AQ GL +VGV L +F+L E AML AI +HRPA+T++AYPNNPTATLWDE Sbjct: 122 GFVMYAMCAQQHGLQYVGVDLDGEFQLREQAMLDAIAEHRPALTFLAYPNNPTATLWDEA 181 Query: 183 AVQRIIDAAGAQGGIVVMDEAYQPFASRTWIDRMRAEPARNAHVLLMRTLSKFGLAGVRL 242 VQRI DA GGIVVMDEAYQPFASR+WIDRMRAEPARN HVLLMRTLSKFGLAGVRL Sbjct: 182 VVQRIADAVAEVGGIVVMDEAYQPFASRSWIDRMRAEPARNGHVLLMRTLSKFGLAGVRL 241 Query: 243 GYLIGPSAFVSEIDKVRPPYNVSVLNCEAALFALEHAEVFAAQAAEIRVERATLIAALRQ 302 GY+IGP+A V EIDK+RPPYNVSVLNCEAALFALEHA VFAAQAAE+R R L+AALR Sbjct: 242 GYMIGPAALVHEIDKLRPPYNVSVLNCEAALFALEHAGVFAAQAAELRAARTDLLAALRA 301 Query: 303 MPGVEKCWDSEANMVLIRVADSAKAYEGMKNRKVLVKNVSTMHPLLANCLRLTVGNAEDN 362 MPGVEK WDS+ANMVL+RVADSA+AYEGMK K+LVKNVSTMHP LANCLRLTVG+ DN Sbjct: 302 MPGVEKVWDSQANMVLVRVADSARAYEGMKACKILVKNVSTMHPSLANCLRLTVGSHADN 361 Query: 363 AQMLAALQASL 373 AQMLAALQASL Sbjct: 362 AQMLAALQASL 372 Lambda K H 0.321 0.134 0.392 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: 515 Number of extensions: 14 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: 373 Length of database: 372 Length adjustment: 30 Effective length of query: 343 Effective length of database: 342 Effective search space: 117306 Effective search space used: 117306 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