Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_069662106.1 BCR25_RS00385 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_001730305.1:WP_069662106.1 Length = 426 Score = 280 bits (715), Expect = 2e-79 Identities = 164/413 (39%), Positives = 242/413 (58%), Gaps = 12/413 (2%) Query: 379 QKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMKE 438 ++T EI V II+ V G+ AL Y+++FD V L++ ++ E+ ++ + E+ Sbjct: 24 EETKEIEEQVKQIIQTVEQNGDQALKNYSKQFDQVVLTDLAVSEEEIEQGYQRVEPEVIA 83 Query: 439 ALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALML 498 +L + EN+ +H Q + + E + GV+ + P+E+VG+Y+PGGTA PS+ LM Sbjct: 84 SLIAAKENIISYHKKQKQYDFFDTE-KAGVIRGQLVLPLERVGVYVPGGTAAYPSSVLMN 142 Query: 499 GVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKV-GASKIVLAGGAQAVAAMAYGTET 557 +PA++A KEI+ +PP S P+V+ A K+ G I GGAQAVAA+AYGTE+ Sbjct: 143 VLPAKIAGVKEIIMVTPPTTSG---IPDVILAAAKIAGVDNIFQIGGAQAVAALAYGTES 199 Query: 558 IPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLS 617 IPKVDKI+GPGN +V AK V L IDM AGPSE+ +IAD+ A+ +VA+DLLS Sbjct: 200 IPKVDKIVGPGNVYVATAKKQVFG----LVGIDMIAGPSEIGIIADDTANPVYVAADLLS 255 Query: 618 QAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEE 676 QAEH ++ ILV S++ +++ + Q LPR I K I+ H I++ E Sbjct: 256 QAEHDTLARAILV--TNSKRFADQVEKEIEQQLKTLPRKTIAEKAISDHGRIIIVPTLEA 313 Query: 677 ALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYA 736 + N+ APEHL +Q+++ Y+ + +AGS+F+GAY E GDY SGTNH LPT G A Sbjct: 314 MFTVMNEIAPEHLEVQLSDPMSYLHEIKHAGSIFLGAYASEPVGDYFSGTNHVLPTSGTA 373 Query: 737 RQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789 + YS F K+ T E L A+ +A+KEGL+ H A+ R + Sbjct: 374 KFYSPLGVYDFVKYSQVTYYTKEALAQAKDAITTLARKEGLEAHARAIDCRFN 426 Lambda K H 0.315 0.133 0.371 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: 725 Number of extensions: 42 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 799 Length of database: 426 Length adjustment: 36 Effective length of query: 763 Effective length of database: 390 Effective search space: 297570 Effective search space used: 297570 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: 42 (22.0 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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