Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_072907092.1 BUB13_RS06015 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_900142125.1:WP_072907092.1 Length = 429 Score = 272 bits (696), Expect = 2e-77 Identities = 168/412 (40%), Positives = 236/412 (57%), Gaps = 16/412 (3%) Query: 384 IMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEG----LTEEMKEA 439 I V II +VR +G+ AL E T KFD KL V + EE E ++ E A Sbjct: 29 IEETVKNIIADVRKRGDVALFELTAKFD--KLELDVDSLEVTEEEIEAAMAQISAESLSA 86 Query: 440 LDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLG 499 L L+ E + +HA Q ET + VL + RP+++VG+Y+PGG A PS+ LM Sbjct: 87 LQLAAERIADYHAKQ-KQETWISTDESDVLVGQMVRPLDRVGIYVPGGKATYPSSVLMNA 145 Query: 500 VPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIP 559 VPA+VA +E++ P +G+V+P V+ A+ G +I GGAQAVAA+AYGT+++P Sbjct: 146 VPAKVAGVEEVIMVVP--MPNGEVNPHVLAAAKISGVDRIFKLGGAQAVAALAYGTDSVP 203 Query: 560 KVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQA 619 +VDKI GPGN +V AK V IDM AGPSE+LVI D + +A+DLLSQA Sbjct: 204 RVDKITGPGNIYVATAKQLVFGQVD----IDMIAGPSEILVINDGSGNAAHIAADLLSQA 259 Query: 620 EHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEEAL 678 EH D V V EK +Q V Q +L R I RK I + I+L +EA+ Sbjct: 260 EH--DELASSVLVTSCEKMAAAVQAEVEKQLSELSREGIARKSIDDYGAIILAQNLDEAI 317 Query: 679 EMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQ 738 SN+ APEHL L + + D + + +AG+VF+G +TPE+ GDY +G NHTLPT G AR Sbjct: 318 AFSNRIAPEHLELAVDSPFDILPQIKHAGAVFMGHHTPEAAGDYLAGPNHTLPTGGTARF 377 Query: 739 YSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSK 790 +S + F K + + + GL+ +G ++ +A+ EGL+ H +V IR+ K Sbjct: 378 FSPLSLDDFVKKSSIVSFSQAGLQRLGNEIVHIAELEGLEAHAKSVSIRLKK 429 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: 702 Number of extensions: 25 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: 429 Length adjustment: 36 Effective length of query: 763 Effective length of database: 393 Effective search space: 299859 Effective search space used: 299859 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