Align Histidinol-phosphate aminotransferase 1; EC 2.6.1.9; Imidazole acetol-phosphate transaminase 1 (uncharacterized)
to candidate WP_011814644.1 HHAL_RS09385 threonine-phosphate decarboxylase
Query= curated2:Q46Y48 (376 letters) >NCBI__GCF_000015585.1:WP_011814644.1 Length = 341 Score = 82.8 bits (203), Expect = 1e-20 Identities = 100/344 (29%), Positives = 147/344 (42%), Gaps = 32/344 (9%) Query: 27 GKPISEVAREFGLDEAGIVKLASNENPLGMPESAKHAAAAAIAELGRYPDSNGFELKAAL 86 G + + FGL G V L++ NP P A A R P+++ E +AA Sbjct: 14 GGNLDQATARFGLPREGWVDLSTGINPTPFP-----LTPAPDAAWHRLPEADDLEARAAE 68 Query: 87 STKLGVPQDWLTLGNGSNDILELAAHALVTPGQSIVYAEYSFAVYALATQEIGARAIVVK 146 + G + GS + L AL PG + A +A +A A Q G R + Sbjct: 69 HYRAG--NNAALALPGSQAAISLLP-ALEPPGYVAIPAP-EYAEHARAWQRWGHRVERLT 124 Query: 147 ARDYGHDLDAMAAAITSDTRLVFIANPNNPTGTFVPAAALETFLAKVPAEV-VVVLDEAY 205 A D A + + +++PNNPTGT AA L + + AE +++DEA+ Sbjct: 125 A-----DCIAAGPPRRLPWQTMVLSHPNNPTGTRHSAATLLAWCDALAAEGGQLIVDEAF 179 Query: 206 NEYLDDDQQYDSVAWVRRYPNLLVSRTFSKAYGLAGLRIGYAVAQPELTDLLNRIRQPFN 265 D + S+A P L++ R+ K YGLAG R+G+ + L L + P+ Sbjct: 180 C----DAEPETSLAPSAGRPGLVLLRSLGKFYGLAGARVGFLLGPQALRQRLADLLGPWP 235 Query: 266 VNSVAQAAAVAALGDTAFLQRSAELNRAGKAQLVEAFSRLGLEFVASSGNFVLVRVGDDD 325 V A+ AA AL D+A+ R + A +L +R GL A +G L R Sbjct: 236 VAGPARHAARQALADSAWQDRQRHVLAASSERLDHLLTRAGL---APTGGTALFRWTPCH 292 Query: 326 DAGARVNVALLRQGVIVR----PVG-NYGMP----RWLRVTIGL 360 DA R L R G+ VR P G +G+P W R+ L Sbjct: 293 DARQR-QAELARAGIWVRAFDAPAGLRFGLPGPESDWQRLAAAL 335 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: 326 Number of extensions: 15 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: 376 Length of database: 341 Length adjustment: 29 Effective length of query: 347 Effective length of database: 312 Effective search space: 108264 Effective search space used: 108264 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 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