Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_011317709.1 AVA_RS04335 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000204075.1:WP_011317709.1 Length = 431 Score = 251 bits (640), Expect = 8e-71 Identities = 159/435 (36%), Positives = 235/435 (54%), Gaps = 13/435 (2%) Query: 361 VVKASDK---VGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSN 417 V+K +D+ Q +S + T ++ V I+ +V+ G++A+ EYT +FD + Sbjct: 3 VLKTTDQEFSTRFQSLVSDRREATVDVSGTVRDILAHVKAHGDAAVQEYTSRFDHYSPHS 62 Query: 418 PVLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPI 477 L+A F E + E+K A++L+ E + FH QLP + +T GV + Sbjct: 63 HHLSAAFIAEQAAKCSAEVKAAIELAAERISSFHQKQLPQDIGYTDTV-GVKLGLNWVAL 121 Query: 478 EKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGAS 537 +VG+Y+PGG A PS+ LM +PA++A + IV P G+++P V+ A+ G + Sbjct: 122 SQVGIYVPGGRASYPSSVLMNALPAKIAGVERIVMTVP--MPHGEINPAVLAAAQVAGVT 179 Query: 538 KIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSE 597 +I GGAQAV A+AYGTETI VDKI+GPGN +V AK V ID AGPSE Sbjct: 180 EIYSIGGAQAVGALAYGTETITPVDKIVGPGNAYVAEAKRQVFGTV----GIDSIAGPSE 235 Query: 598 VLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVD 657 +LV+AD + +++A DLLSQAEH +Q IL+ SE Q++ AV LP Sbjct: 236 ILVVADRQNNPEWIAWDLLSQAEHDPSAQSILI--TDSESFAQQVIGAVEQILTTLPTTK 293 Query: 658 IVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTP 716 + H +++ E++ + NQ APEH+ L + N + AGS+F+G YTP Sbjct: 294 VASSSWQNHGAVIIVRDLAESIPLLNQLAPEHVELCVDNPQLLASQIKCAGSLFLGRYTP 353 Query: 717 ESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEG 776 E+ GDY G NH LPT AR SG + F K IT L+ IG++ + +A+ EG Sbjct: 354 EAIGDYLGGPNHVLPTSRSARFASGLSVYDFLKRITYLECNQAALQAIGQSAVTLAETEG 413 Query: 777 LDGHRNAVKIRMSKL 791 L H +V +R+ L Sbjct: 414 LPAHAGSVAVRLQGL 428 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: 650 Number of extensions: 26 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: 431 Length adjustment: 37 Effective length of query: 762 Effective length of database: 394 Effective search space: 300228 Effective search space used: 300228 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 25 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