Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_027179304.1 G496_RS0110795 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000429985.1:WP_027179304.1 Length = 434 Score = 250 bits (639), Expect = 1e-70 Identities = 153/412 (37%), Positives = 235/412 (57%), Gaps = 14/412 (3%) Query: 382 SEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEY--FEGLTEEMKEA 439 S++ +V I+ NVR G+SAL+EYT KFD + ++ + F + E E Sbjct: 29 SKVDDIVREILANVRKNGDSALIEYTRKFDCPDFNESMMRVSLDQMSMAFAEVKNEDLEI 88 Query: 440 LDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTA---ILPSTAL 496 ++ SI NVR FH Q+ E+ + G + + RP+++VGLY+PGG L S+ + Sbjct: 89 IEESIRNVRDFHRRQVE-ESWMTTKEDGTILGQIVRPVDRVGLYVPGGQGGETPLISSMI 147 Query: 497 MLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTE 556 M VPAQVA KEI SPPRK DG ++P ++ A+++G +++ ++G A A+AA+AYGTE Sbjct: 148 MNAVPAQVAGVKEIAVISPPRK-DGTLNPYIIATAKELGINEVYVSGSAWAIAALAYGTE 206 Query: 557 TIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLL 616 TI D I GPGN FV AK + + IDM AGPSE+ +IAD A+ + A+D+L Sbjct: 207 TIKPCDVIAGPGNVFVATAKSQLVGEV----GIDMIAGPSEIAIIADSSANPIWTAADML 262 Query: 617 SQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYE 675 SQAEH + IL+ N E +++ + + QA +LPR +I K +A IV + Sbjct: 263 SQAEHDPLASSILITDN--EALAEKVTEELSLQASRLPRGEIALKSLAAWGAIVTVNSMN 320 Query: 676 EALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGY 735 A+++ N+ APEHL L +++ + + +AG++F+G + PE GDY +G NH LPT G Sbjct: 321 AAIDLVNRIAPEHLELSVSDPWSILGRISHAGAIFMGHHCPEPVGDYFAGPNHVLPTVGT 380 Query: 736 ARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787 AR S + TF K + + G + +A+ EGL+ H +++ R Sbjct: 381 ARFSSALSVETFCKKSSLIYTDKNYVTRHGAKIARMARLEGLEAHARSIESR 432 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: 701 Number of extensions: 35 Number of successful extensions: 7 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 10 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