Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_086509840.1 BZY95_RS10280 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_002151265.1:WP_086509840.1 Length = 441 Score = 262 bits (669), Expect = 3e-74 Identities = 154/411 (37%), Positives = 232/411 (56%), Gaps = 13/411 (3%) Query: 382 SEIMHLVNPIIENVRDKGNSALLEYTEKFDGV---KLSNPVLNAPFPEEYFEGLTEEMKE 438 +E+ V II V+ +G++AL+EYT++FD + ++ L A E+ + GL E+ ++ Sbjct: 37 AEVQERVAEIIAAVKVRGDAALVEYTQRFDRLAVGSMAELTLGADRLEQAYRGLPEQQRD 96 Query: 439 ALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALML 498 AL + E +R +H Q P E VL + P+++ G+Y+PGG A PS+ LM Sbjct: 97 ALAQAAERIRLYHERQKPESWSYTEADGSVLGQQVT-PLDRAGIYVPGGKAAYPSSVLMN 155 Query: 499 GVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETI 558 +PA VA +EIV P DG ++ V+ A G + GGAQAVAA+AYGTE++ Sbjct: 156 AIPAHVAGVREIVMVVPT--PDGVLNELVLAAAHLAGVDHVFTIGGAQAVAALAYGTESV 213 Query: 559 PKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQ 618 P+VDKI+GPGN +V AK V IDM AGPSE+LV++D D D++A DL SQ Sbjct: 214 PRVDKIVGPGNIYVATAKRAVFGQV----GIDMIAGPSEILVVSDGGTDPDWLAMDLFSQ 269 Query: 619 AEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYEEA 677 AEH D+Q +LV + E + ++ ++ L R IVR+ +A ++ C +EA Sbjct: 270 AEHDEDAQALLV--SWDESHLDRVEASIARLLPTLEREAIVRESLARRGALIHCRDRDEA 327 Query: 678 LEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYAR 737 +++ N+ APEHL L +A + V +AG++F+G YT E+ GDY +G NH LPT G AR Sbjct: 328 VQLINRIAPEHLELSLAEPEAMLPQVRHAGAIFMGRYTAEALGDYCAGPNHVLPTSGTAR 387 Query: 738 QYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 S FQK + + + G +GR +A+ E L H + + R+ Sbjct: 388 FSSPLGVYDFQKRSSIIHCSEAGASTLGRVASVLARGESLTAHARSAEYRI 438 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: 717 Number of extensions: 32 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: 441 Length adjustment: 37 Effective length of query: 762 Effective length of database: 404 Effective search space: 307848 Effective search space used: 307848 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