Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate GFF871 PS417_04420 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__WCS417:GFF871 Length = 440 Score = 256 bits (653), Expect = 2e-72 Identities = 146/403 (36%), Positives = 235/403 (58%), Gaps = 15/403 (3%) Query: 391 IIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFE----GLTEEMKEALDLSIEN 446 II+ VR++G++AL+++T +FDG+ +++ + + P E E +T +EAL+++ Sbjct: 42 IIKAVRERGDAALVDFTRQFDGLDVAS-MSDLILPRERLELALTRITAPQREALEVAAAR 100 Query: 447 VRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQ 506 VR +H Q E VL + P+++ GLY+PGG A PS+ LM +PA+VA Sbjct: 101 VRSYHEKQKQDSWSYTEADGTVLGQKVT-PLDRAGLYVPGGKASYPSSVLMNAIPAKVAG 159 Query: 507 CKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILG 566 E+V P + G+++ V+ A G ++ GGAQAVAA+AYGTE++PKVDK++G Sbjct: 160 VTEVVMVVPTPR--GEINELVLAAACIAGVDRVFTIGGAQAVAALAYGTESVPKVDKVVG 217 Query: 567 PGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQ 626 PGN +V AK +V IDM AGPSE+LV+ D D D++A DL SQAEH D+Q Sbjct: 218 PGNIYVATAKRHVFGQV----GIDMIAGPSEILVVCDGQTDPDWIAMDLFSQAEHDEDAQ 273 Query: 627 VILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI-AHSTIVLCDGYEEALEMSNQYA 685 ILV + + + ++ +++ + R +I+ K I ++L E+A+E++N+ A Sbjct: 274 AILVSPDA--EFLDKVAASINKLLPTMDRAEIIEKSINGRGALILVRDMEQAIEVANRIA 331 Query: 686 PEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTA 745 PEHL L +A+ ++ + +AG++F+G +T E+ GDY +G NH LPT G AR S Sbjct: 332 PEHLELSVADPQAWLPSIRHAGAIFMGRHTSEALGDYCAGPNHVLPTSGTARFSSPLGVY 391 Query: 746 TFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 FQK + +P+G +G+ +A+ E L H + + R+ Sbjct: 392 DFQKRSSIIFCSPQGASELGKTASVLARGESLSAHARSAEYRI 434 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: 719 Number of extensions: 41 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: 440 Length adjustment: 37 Effective length of query: 762 Effective length of database: 403 Effective search space: 307086 Effective search space used: 307086 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 09 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