Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_037581586.1 BS73_RS28925 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000744815.1:WP_037581586.1 Length = 435 Score = 241 bits (616), Expect = 5e-68 Identities = 150/407 (36%), Positives = 225/407 (55%), Gaps = 18/407 (4%) Query: 388 VNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMKEALDLSIENV 447 V PI E+V +G AL+E TE+FDGV+L+ + + L +++ AL++SIE Sbjct: 32 VRPICEDVHHRGVEALIEITERFDGVRLTTTRVPVEELHKALAELDPKVRAALEVSIERA 91 Query: 448 RKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQC 507 RK H Q T+ G + R+ P+E+VGLY+PGG A+ PS+ +M VPAQ A Sbjct: 92 RKVHREQRRTDHTTQVVPGGTVTERWV-PVERVGLYVPGGRAVYPSSVVMNVVPAQEAGV 150 Query: 508 KEIVFASPPRKS-DGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILG 566 + + SPP+ DG P ++ +G ++ GGAQAVA AYGTE V+ + G Sbjct: 151 ESLAVTSPPQPDFDGLPHPTILAACALLGVDEVYAVGGAQAVAMFAYGTEECRPVNLVTG 210 Query: 567 PGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQ 626 PGN +V AAK ++ ID AGP+E+ ++AD AD VA+D++SQAEH + Sbjct: 211 PGNIWVAAAKRLLKGRI----GIDAEAGPTEIAILADSTADPRHVAADMISQAEHDPLAA 266 Query: 627 VILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA------HSTIVLCDGYEEALEM 680 +LV +L+ + DAV + R + IA S IVL D ++ L++ Sbjct: 267 AVLVTDSLA------LADAVEKELEPQVRATKHSERIATALDGRQSGIVLVDDIDQGLKV 320 Query: 681 SNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYS 740 + YA EHL +Q A+A+ V NAG++F+GA+ P S GDY++G+NH LPT G A S Sbjct: 321 VDAYAAEHLEIQTADAHAVAARVRNAGAIFIGAWAPVSLGDYAAGSNHVLPTGGCACHSS 380 Query: 741 GANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787 G + +F + I + + E L + V+ +A E L GH +A++ R Sbjct: 381 GLSVQSFLRGIHVVDYSREALAEVAGHVVNLANAEDLPGHGDAIRAR 427 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: 668 Number of extensions: 31 Number of successful extensions: 6 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 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