Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_037576905.1 BS73_RS27295 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000744815.1:WP_037576905.1 Length = 439 Score = 199 bits (505), Expect = 3e-55 Identities = 133/414 (32%), Positives = 211/414 (50%), Gaps = 10/414 (2%) Query: 377 PIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEM 436 P Q+ ++ V+ ++ ++ G A+L Y+ + DG + + ++A + + L+ E+ Sbjct: 27 PAQRLPAVVETVSRMLSDIEKNGMDAVLRYSRELDGWQGGDVEISAAELKRTGDSLSPEL 86 Query: 437 KEALDLSIENVRKFHAAQLP-TETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTA 495 ++AL E R F Q + E E PGV+ + P+ +VG Y+P G + ++A Sbjct: 87 RQALAAGAERTRLFAVEQREHLQDFETELIPGVVTGQKYLPVPRVGAYLPAGNFPILASA 146 Query: 496 LMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGT 555 M A+ A ++ +PP G P V+Y A G + GG QA+AAMA+G Sbjct: 147 FMTVGVAKAADVPTVLACTPPTAEQGG-HPAVLYAAYLSGVDRAFALGGVQALAAMAFGL 205 Query: 556 ETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDL 615 D ++G GN +VT AK + ID+ AGPSEV VIADE AD + VA+DL Sbjct: 206 LGDQPADMLVGAGNAYVTEAKRQLFGRV----GIDLLAGPSEVAVIADETADPELVAADL 261 Query: 616 LSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGY 674 L QAEHG S L V S + + + V Q QLP DI H T+ + + Sbjct: 262 LGQAEHGRQSPASL--VTTSRELGLAVLEEVEKQLRQLPTRDIAEPAWRDHGTVYVAEDR 319 Query: 675 EEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYS-SGTNHTLPTY 733 + A+E+ + APEHL + A+ + Y + + N GS+F+GA++ + D +GTNH LPT Sbjct: 320 QTAVELMDLLAPEHLEVISADDDYYHQNLKNYGSIFLGAWSTVAYSDKGIAGTNHVLPTG 379 Query: 734 GYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787 AR +G + + F K +T Q ++ E ++ V ++ EG+ HR +R Sbjct: 380 RGARASAGLSVSRFLKPLTFQKVSAEATPDLAAHVEAISDFEGMAAHRATATLR 433 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: 690 Number of extensions: 36 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: 439 Length adjustment: 37 Effective length of query: 762 Effective length of database: 402 Effective search space: 306324 Effective search space used: 306324 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 Jul 26 2024. The underlying query database was built on Jul 25 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