Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_008783672.1 BL_RS00710 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000007525.1:WP_008783672.1 Length = 465 Score = 233 bits (595), Expect = 1e-65 Identities = 147/431 (34%), Positives = 227/431 (52%), Gaps = 20/431 (4%) Query: 373 ALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGL 432 A+ R TSE LV PI+++V+++G +AL ++ EKFD V+ N + ++ L Sbjct: 24 AMPRAAMGTSEATDLVRPILDDVKERGAAALRDFEEKFDHVRPKNLRVPVEAIKDALTTL 83 Query: 433 TEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILP 492 E++ A++ S+ R A Q+P + + + R+ PI++VGLY+PGG A+ P Sbjct: 84 DPEVRAAIEESVRRARAVAANQVPKDFYTDLAEGARVAERWI-PIQRVGLYVPGGKAVYP 142 Query: 493 STALMLGVPAQVAQCKEIVFASPPRKS--DGKVSPEVVYVAEKVGASKIVLAGGAQAVAA 550 S+ +M VPAQ A + + A+PP + +G + ++ +G ++ GGAQA+A Sbjct: 143 SSVIMNAVPAQAAGVESLAIATPPARDNEEGLPNKTILATCAILGVDEVYAVGGAQAIAM 202 Query: 551 MAYGTE---------TIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVI 601 AYG + VDKI GPGN FV AK V A ID AGP+E+ +I Sbjct: 203 FAYGAKGSEPQDGDILCDPVDKITGPGNIFVATAKSLVS----AFVGIDAVAGPTEIGII 258 Query: 602 ADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRK 661 ADE A+ +A+DL+ QAEH D V S + ++Q+++ + + + V Sbjct: 259 ADETANPSLLAADLIGQAEH--DELAGSVLFTDSTEIADKVQESLKYRVPRTEHAERVHT 316 Query: 662 CIA--HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESC 719 ++ S IVL DG +++++ +N YA EHL +Q +A+ VK + NAG++F G Y+P Sbjct: 317 SLSGTQSAIVLTDGLDQSIDAANAYAAEHLEIQTKDADAVVKRIKNAGAIFRGPYSPVPL 376 Query: 720 GDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDG 779 GDY SG+NH LPT G AR +G TF K + EGL+ + + A E L Sbjct: 377 GDYMSGSNHVLPTGGTARFAAGLGVHTFMKPVEVIEYDEEGLKALAARINAFAVSEDLPA 436 Query: 780 HRNAVKIRMSK 790 H V R K Sbjct: 437 HGECVLSRFVK 447 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: 767 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: 465 Length adjustment: 37 Effective length of query: 762 Effective length of database: 428 Effective search space: 326136 Effective search space used: 326136 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 12 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