Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 3607568 Dshi_0979 Histidinol dehydrogenase (RefSeq)
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Dino:3607568 Length = 438 Score = 263 bits (671), Expect = 2e-74 Identities = 172/448 (38%), Positives = 244/448 (54%), Gaps = 30/448 (6%) Query: 356 PIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKL 415 P+ L +A + + L+ + ++ V II +VR +G++A++E T +FD + L Sbjct: 2 PLFLSSAEAGFEAAFAQLLTMKREDAVDVDDTVAGIIADVRARGDAAVIELTSRFDRLTL 61 Query: 416 SNPVLNAPFPEEYFE--GLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRF 473 + L E E ++EE + AL+L+ E +R +HA Q+P + E L R+ Sbjct: 62 TPQTLAFSAEEIAAEIAKVSEEDRAALELAAERIRAYHARQMPQDARWTEPTGAELGWRW 121 Query: 474 PRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEK 533 P+ GLY+PGG A PS+ LM +PAQVA + +V +P DG V+P V+ A Sbjct: 122 T-PVSAAGLYVPGGLASYPSSVLMNAIPAQVAGVERLVICAPT--PDGVVNPLVLLAASL 178 Query: 534 VGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPA 593 G + GGAQA+AA+AYGTETI VDKI GPGN FV AAK V IDM A Sbjct: 179 SGVDTVYRVGGAQAIAALAYGTETIAPVDKITGPGNAFVAAAKRRVFGRV----GIDMIA 234 Query: 594 GPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQL 653 GPSE+LVIAD D D D++A DLLSQAEH +Q IL+ DA QA+ Sbjct: 235 GPSEILVIADRDNDPDWIAVDLLSQAEHDESAQSILI-----------TDDAAFGQAVAA 283 Query: 654 P---RVDIV-RKCIA------HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLV 703 R++ + R+ IA ++ EA E+SN+ APEHL L +A+ + + + Sbjct: 284 AVEARLETLERRAIAGPSWRDFGAVITVRDLAEAAELSNRIAPEHLELCVADPDGLAEHI 343 Query: 704 DNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLEN 763 +AG++F+GA+TPE+ GDY G NH LPT AR SG + F K T +TP L Sbjct: 344 THAGAIFLGAWTPEAIGDYIGGPNHVLPTARSARFSSGLSVMDFVKRTTLAKMTPAALAE 403 Query: 764 IGRAVMCVAKKEGLDGHRNAVKIRMSKL 791 IG A +A E L+ H +V+ R+ +L Sbjct: 404 IGPAAERLAISESLEAHGLSVRARLDRL 431 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: 609 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: 438 Length adjustment: 37 Effective length of query: 762 Effective length of database: 401 Effective search space: 305562 Effective search space used: 305562 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 09 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