Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_035629294.1 P166_RS0104935 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000711315.1:WP_035629294.1 Length = 435 Score = 251 bits (640), Expect = 8e-71 Identities = 151/428 (35%), Positives = 234/428 (54%), Gaps = 13/428 (3%) Query: 367 KVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPV-LNAPFP 425 K ++K L+ + +V +I NVR +G+ ALLEYT KFD + L L P Sbjct: 17 KPELEKLLAWETVSNESVNSVVKDVIHNVRTRGDEALLEYTAKFDRLSLEKGSDLEVPKA 76 Query: 426 E--EYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLY 483 E + ++ K+ L+L+ + V+ +H Q+ ++ G + + ++ VGLY Sbjct: 77 ELTAALNRIPQDQKDGLELAAQRVKDYHENQI-MKSWSYREADGTMLGQQVTALDSVGLY 135 Query: 484 IPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAG 543 +PGG A PS+ +M VPA+VA K+++ P DG+V+ V+ A G ++ G Sbjct: 136 VPGGKAAYPSSVIMNAVPAKVAGVKDLIMVVPT--PDGEVNDMVLAAAAICGVDRVFKLG 193 Query: 544 GAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIAD 603 GAQAVAA+AYGTET+P VDKI+GPGN +V AK + IDM AGPSE+LV D Sbjct: 194 GAQAVAALAYGTETVPCVDKIVGPGNIYVATAK----REVFGAVGIDMIAGPSEILVYCD 249 Query: 604 EDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI 663 D D++A DL SQAEH D+Q ILV + +++ ++++ ++PR I+ K + Sbjct: 250 GQTDPDWIAVDLFSQAEHDEDAQSILV--TQDAEFAEKVYESMNKLISEMPRQAIITKAL 307 Query: 664 A-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDY 722 I++ + ++A+++ N APEHL L I + + + +AG++F+G YT E+ GDY Sbjct: 308 EDRGAIIVVENEDQAIDLINYIAPEHLELSIEDPEALLPKIKHAGAIFMGRYTAEALGDY 367 Query: 723 SSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRN 782 +G NH LPT AR S FQK + + EG +G+ +A EGL H Sbjct: 368 CAGPNHVLPTSRTARFSSPLGVYDFQKRSSLIMCSAEGANLLGQVAGVLADGEGLQAHAA 427 Query: 783 AVKIRMSK 790 + + R+ K Sbjct: 428 SARYRVKK 435 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: 790 Number of extensions: 45 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: 435 Length adjustment: 37 Effective length of query: 762 Effective length of database: 398 Effective search space: 303276 Effective search space used: 303276 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