Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_086508840.1 BZY95_RS04815 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_002151265.1:WP_086508840.1 Length = 436 Score = 214 bits (544), Expect = 1e-59 Identities = 142/413 (34%), Positives = 215/413 (52%), Gaps = 11/413 (2%) Query: 383 EIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMKEALDL 442 ++ V ++ + +G+ A+ E +EKFD + L+ E LT + + + Sbjct: 20 KVRETVEQTLQAIETRGDEAVRELSEKFDRWSPATFRLSQAEIERAISELTAQELDDIRF 79 Query: 443 SIENVRKFHAAQLPT-ETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVP 501 + +R+F AQL + + +EVET+PGV+ P+ VG Y+PGG + ++A M + Sbjct: 80 AQAQIRRFAEAQLASMQDVEVETRPGVVLGHKHIPVNSVGCYVPGGAYPMVASAHMSVLT 139 Query: 502 AQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKV 561 A+VA K ++ A+PP + GK P +V GA +I++ GG QAV AMA GTE+I V Sbjct: 140 AKVAGVKRVIAAAPPYQ--GKPHPAIVAAMHLAGADEILVLGGVQAVGAMAIGTESIEAV 197 Query: 562 DKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEH 621 D ++GPGN FV AK + ID+ AGP+E LVIADE D A+DLL QAEH Sbjct: 198 DMLVGPGNAFVAEAKRQLFGRV----GIDLFAGPTETLVIADETVDGLLCATDLLGQAEH 253 Query: 622 GIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEEALEM 680 G S L+ SE + A+ +LP +I R+ + +++CD +EE L++ Sbjct: 254 GPTSPAALL--TNSEALAKATLTAIDELLAKLPTAEIARQAWNDYGEVIVCDSHEEMLQV 311 Query: 681 SNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYS 740 +++ A EH+ + + N Y+ + N G++F+G T + GD GTNHTLPT AR Sbjct: 312 ADEMAYEHVQVMTEDPNLYLDRLTNYGALFLGPRTNVAYGDKVIGTNHTLPTRKAARYTG 371 Query: 741 GANTATFQKFITAQNI-TPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKLG 792 G F K T Q + T E IG + EG GH R+ + G Sbjct: 372 GLWVGKFLKTCTYQKVLTDEASAEIGSYCSRLCALEGFAGHGEQANERVRRYG 424 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: 678 Number of extensions: 27 Number of successful extensions: 4 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: 436 Length adjustment: 37 Effective length of query: 762 Effective length of database: 399 Effective search space: 304038 Effective search space used: 304038 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