Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_011841567.1 RSPH17029_RS11520 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000015985.1:WP_011841567.1 Length = 434 Score = 248 bits (632), Expect = 6e-70 Identities = 166/446 (37%), Positives = 239/446 (53%), Gaps = 26/446 (5%) Query: 356 PIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKL 415 P LD + + L + + ++ +V II +VR +G++A++E T +FD ++L Sbjct: 2 PQFLDTRRPGFEADFTALLGMKREDSPDVDAVVAGIIADVRARGDAAVIELTARFDRLEL 61 Query: 416 SNPVLNAPFPEEYFEG----LTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCS 471 + L F E E ++ E + AL+L+ E +R +HA Q+P + L Sbjct: 62 TPERL--AFSEAEIEAEIATVSAEDRAALELAAERIRAYHARQMPENARWTDAAGAELGW 119 Query: 472 RFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVA 531 R+ PI GLY+PGG A PS+ LM +PA+VA + +V A P G V+P V+ A Sbjct: 120 RWG-PIASAGLYVPGGLASYPSSVLMNAIPARVAGVERLVVACPT--PGGVVNPLVLLAA 176 Query: 532 EKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDM 591 G + GGAQAVAA+AYGTETI VDKI GPGN +V AAK V IDM Sbjct: 177 RLAGVDAVYRIGGAQAVAALAYGTETIRPVDKITGPGNAYVAAAKRRVFGRV----GIDM 232 Query: 592 PAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQAL 651 AGPSE+LVIA+ D D++A DLLSQAEH +Q ILV + E QA+ Sbjct: 233 IAGPSEILVIAEGAVDPDWIALDLLSQAEHDESAQSILVTPD-------EALGRAVVQAV 285 Query: 652 QLPRVDIVRKCIA------HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDN 705 + + R+ IA + +++ EEA +S++ APEHL L +A+ + + Sbjct: 286 EARLETLERRAIAGASWRDYGAVIVTRDLEEAAALSDRVAPEHLELYVADPEALAARIRH 345 Query: 706 AGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIG 765 AG++F+GA+TPE+ GDY G NH LPT AR SG + F K T +TP L +G Sbjct: 346 AGAIFLGAWTPEAIGDYVGGPNHVLPTARSARFSSGLSVMDFLKRTTLARMTPAALRAVG 405 Query: 766 RAVMCVAKKEGLDGHRNAVKIRMSKL 791 A +A E L+ H +V+ R+ +L Sbjct: 406 PAAERLAISESLEAHGLSVRARLDRL 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: 630 Number of extensions: 29 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: 434 Length adjustment: 37 Effective length of query: 762 Effective length of database: 397 Effective search space: 302514 Effective search space used: 302514 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 16 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