Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_019556883.1 F612_RS0106150 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000381085.1:WP_019556883.1 Length = 433 Score = 249 bits (635), Expect = 3e-70 Identities = 153/409 (37%), Positives = 226/409 (55%), Gaps = 13/409 (3%) Query: 384 IMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF---EGLTEEMKEAL 440 I +V ++ +VR G++ALLEYT KFD + L++ E F E + + ++AL Sbjct: 32 INDVVKEVVNSVRLNGDTALLEYTAKFDRLSLNSAAELEISKERLFAALERIPADQRQAL 91 Query: 441 DLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGV 500 + S + VR +H Q+ + E G + + P++ VGLY+PGG A PS+ +M + Sbjct: 92 ETSAKRVRDYHERQVQA-SWSYEEADGTMLGQQVTPLDSVGLYVPGGKAAYPSSVIMNAI 150 Query: 501 PAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPK 560 PA+VA + ++ P DG+VS V+ A + GGAQAVAA+AYGTET+P Sbjct: 151 PAKVAGVETLIMVVPT--PDGEVSDMVLAAAAICDVDAVFTLGGAQAVAALAYGTETVPA 208 Query: 561 VDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAE 620 VDKI+GPGN +V AK V IDM AGPSE+LV D + D++A DL SQAE Sbjct: 209 VDKIVGPGNIYVATAKRMVFGTV----GIDMIAGPSEILVYCDGKTNPDWIAVDLFSQAE 264 Query: 621 HGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEEALE 679 H D+Q ILV + + ++ ++++ +PR I+RK + I++ + E+ALE Sbjct: 265 HDEDAQSILVTPDA--EFADKVLESMNRLLPTMPRQTIIRKALEDRGAIIVVNDEEQALE 322 Query: 680 MSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQY 739 M N APEHL L I N + + +AG++F+G +T E+ GDY +G NH LPT AR Sbjct: 323 MINLIAPEHLELSIENPKALLPKIRHAGAIFMGRFTAEAIGDYCAGPNHVLPTSRTARFS 382 Query: 740 SGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 S FQK + + EG +GR +A EGL H + + R+ Sbjct: 383 SPLGVYDFQKRSSLIMCSAEGANTLGRIAGVLADGEGLQAHAASARYRI 431 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: 736 Number of extensions: 38 Number of successful extensions: 5 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: 799 Length of database: 433 Length adjustment: 37 Effective length of query: 762 Effective length of database: 396 Effective search space: 301752 Effective search space used: 301752 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 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