Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_007472909.1 CMTB2_RS00390 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000170735.1:WP_007472909.1 Length = 429 Score = 263 bits (671), Expect = 2e-74 Identities = 161/435 (37%), Positives = 246/435 (56%), Gaps = 20/435 (4%) Query: 359 LDVVKASDK---VGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDG--- 412 + V+K +DK Q+ L+R S + ++V II V+++GN AL + KFD Sbjct: 1 MKVIKTTDKNFTKEFQEILNRGKMDISNVENIVKEIINEVKNEGNKALFRHISKFDKWTP 60 Query: 413 VKLSNPVLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSR 472 K + ++ ++ ++ L EE+K+AL L+ ++ +H QLP L+ E +L + Sbjct: 61 TKNEDLEISKSEMKKAYDNLDEELKKALHLAYNRIKAYHEKQLPKSWLDFEENGSILGQK 120 Query: 473 FPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAE 532 P+ + G+Y+PGG A PS+ LM +PA VA +EI+ +P + K + ++ Sbjct: 121 VT-PVNRAGVYVPGGKAFYPSSLLMNVIPAIVAGVREIIVTTPV--IENKPNELLLAALY 177 Query: 533 KVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMP 592 GA K GGA A+AA++YGTE+IPKVD I GPGN FV AK V D +IDM Sbjct: 178 ICGAPKTFKVGGASAIAALSYGTESIPKVDVITGPGNIFVATAKKLVYGDV----NIDMI 233 Query: 593 AGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVN--LSEKKIQEIQDAVHNQA 650 AGPSE+ +IAD A D+VA DLLSQAEH + IL+ + L+ K +++I+ + Sbjct: 234 AGPSEIGIIADNSAKPDYVAIDLLSQAEHDEMASSILITDSEMLAIKTLEKIKKFLK--- 290 Query: 651 LQLPRVDIVRKCIAH-STIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSV 709 +L R +I +K I I++ EEA+ N+ APEHL + N + + + NAG++ Sbjct: 291 -ELERREIAQKSIEERGAIIITQNIEEAINFMNEIAPEHLEILTKNPFELLPYIQNAGAI 349 Query: 710 FVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVM 769 F+G YTPE GDY +G NHTLPT G A+ YS N F K + + + + +E +G++ Sbjct: 350 FLGEYTPEPIGDYIAGPNHTLPTGGTAKFYSPLNVEIFMKKSSIISFSKKAMEEMGKSCA 409 Query: 770 CVAKKEGLDGHRNAV 784 +AK EGL H+ +V Sbjct: 410 ILAKTEGLTAHQKSV 424 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: 744 Number of extensions: 34 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: 429 Length adjustment: 36 Effective length of query: 763 Effective length of database: 393 Effective search space: 299859 Effective search space used: 299859 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