Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_046007894.1 OLEAN_RS02340 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000967895.1:WP_046007894.1 Length = 435 Score = 264 bits (675), Expect = 7e-75 Identities = 150/412 (36%), Positives = 236/412 (57%), Gaps = 13/412 (3%) Query: 383 EIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP---VLNAPFPEEYFEGLTEEMKEA 439 ++ +V I+++V+ +G++A++EY+ +FD + + N LN E+ L + + A Sbjct: 32 QVQTIVTDILDDVKTRGDAAVIEYSNRFDHLHVENMDQLELNQEQLEDALNTLPADQRHA 91 Query: 440 LDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLG 499 L + + VRK+H Q ++ + + G L + P+++VG+Y+PGG A PS+ LM Sbjct: 92 LLAAADRVRKYHDKQ-KQDSWQYTEEDGTLLGQKVTPLDRVGIYVPGGKAAYPSSVLMNA 150 Query: 500 VPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIP 559 +PA VA +EI+ P G+++ V+ A G SK+ GGAQA+AA+AYGT T+P Sbjct: 151 IPAHVAGVQEIIMVVPT--PGGELNQLVLAAAAVAGVSKVFTVGGAQAIAALAYGTATVP 208 Query: 560 KVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQA 619 KVDKI+GPGN FV AK V IDM AGPSE+LV+ D D D++A DL SQA Sbjct: 209 KVDKIVGPGNIFVATAKRQVFGTV----GIDMIAGPSEILVVCDGKTDPDWIAMDLFSQA 264 Query: 620 EHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI-AHSTIVLCDGYEEAL 678 EH D+Q IL+ + + + ++Q ++ + R DI+R + A + ++ EA Sbjct: 265 EHDEDAQAILISPD--QNFLDQVQASIEKLLPTMARKDIIRASLNARAALIKVKDMNEAC 322 Query: 679 EMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQ 738 E+SN APEHL L + + + + +AG++F+G +T E+ GDY +G NH LPT G AR Sbjct: 323 EVSNTIAPEHLELSVDDPQALLPQIRHAGAIFMGRHTSEALGDYCAGPNHVLPTSGTARF 382 Query: 739 YSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSK 790 S FQK + +PEG +G+ +A+ E L+GH + + R+ K Sbjct: 383 SSPLGVYDFQKRSSLIMCSPEGASELGKIASVLARGEQLEGHARSAEYRIKK 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: 732 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: 435 Length adjustment: 37 Effective length of query: 762 Effective length of database: 398 Effective search space: 303276 Effective search space used: 303276 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