Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_013538076.1 THEAM_RS06690 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000185805.1:WP_013538076.1 Length = 443 Score = 268 bits (684), Expect = 6e-76 Identities = 161/400 (40%), Positives = 242/400 (60%), Gaps = 12/400 (3%) Query: 391 IIENVRDKGNSALLEYTEKFDGVKLS--NPVLNAPFPEEYFEGLTEEMKEALDLSIENVR 448 IIENVR ++A+ Y +KFD V+L+ N ++ EE F + +E+ +A++ ++E VR Sbjct: 38 IIENVRQFRDTAVFGYAKKFDRVELTPENVKVSEREIEEAFNRVPKEVVKAIEFAVERVR 97 Query: 449 KFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCK 508 +FH Q E T+PG++ + P++ G+Y+PGG A PS+ +M VPA+VA + Sbjct: 98 RFHEHQ--KENSYFVTEPGIVLGQKVTPLDSAGIYVPGGKASYPSSVVMNAVPAKVAGVE 155 Query: 509 EIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPG 568 ++V +P S +V+P + A+ G ++I GGA VAA+A+GTE+IPKVDKI+GPG Sbjct: 156 KVVMITPAIGSL-EVNPYTLVAAKLSGVNEIYRVGGAHGVAAVAFGTESIPKVDKIVGPG 214 Query: 569 NQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVI 628 N +V AK ++ IDM AGPSE+LVIADE A+ D+VA+DLLSQAEH + Sbjct: 215 NIYVALAKKFLFGTVD----IDMVAGPSEILVIADESANPDWVATDLLSQAEHDELAGAF 270 Query: 629 LVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYEEALEMSNQYAPE 687 LV S++ QE+ AV + +L R +I RK I + T+ L + + +++N+ APE Sbjct: 271 LV--THSDRVAQEVVKAVEEKLKKLSRKEIARKAIENFGTVFLTEDVNHSCDVANEIAPE 328 Query: 688 HLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATF 747 HL + + + +AG++F+G YT ES GDY G NH LPT G AR +S F Sbjct: 329 HLEVATKEPFGLLDRIKHAGAIFLGHYTCESLGDYVLGPNHVLPTGGSARFFSPLGVYDF 388 Query: 748 QKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787 K + +TPEG + +G A +A+ EGL+ HR AV++R Sbjct: 389 IKRSSVIYVTPEGFKQVGWAARELAECEGLEAHRLAVEVR 428 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: 807 Number of extensions: 43 Number of successful extensions: 6 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: 443 Length adjustment: 37 Effective length of query: 762 Effective length of database: 406 Effective search space: 309372 Effective search space used: 309372 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