Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_028585589.1 G494_RS0117715 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000429965.1:WP_028585589.1 Length = 436 Score = 268 bits (686), Expect = 4e-76 Identities = 160/443 (36%), Positives = 260/443 (58%), Gaps = 21/443 (4%) Query: 359 LDVVKASDKVG---VQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKL 415 ++VV+A+ K G +++ +R ++ S V+ I++ VR G+ A+LEYT ++D ++ Sbjct: 2 VEVVRAAGKEGQERLERLRNRFVEADSGCRDAVSEILQQVRQDGDQAVLEYTRRYDAPEM 61 Query: 416 SNPVLNAPFPEEYFEGLTEEMK----EALDLSIENVRKFHAAQLPTETLEVETQPGVLCS 471 L PEE FE EE+ E L L+++ +R FH ++ + + + G + Sbjct: 62 ELGGLRVA-PEE-FERAREEVDPAFLETLGLAVQRIRTFHEREMEDSWM-LTREDGTITG 118 Query: 472 RFPRPIEKVGLYIPGG---TAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVV 528 R RP++ GLY+PGG + L S+ LM G+PA +A + V +PP + +G V+P ++ Sbjct: 119 RLVRPVDSAGLYVPGGQGGSTPLVSSVLMNGIPAAIAGVERRVMVTPPNQ-EGLVNPALL 177 Query: 529 YVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCS 588 A ++G S++ G A A+AA+AYGT TIP+VD I+GPGNQ+V AK V + Sbjct: 178 VAAREIGISEVYKTGSAWAIAALAYGTPTIPRVDVIVGPGNQYVAEAKRQVMGRVR---- 233 Query: 589 IDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHN 648 IDM AGPSEVL++AD+ A+ F+A+D+L+QAEH D Q + + S + +E+ + + Sbjct: 234 IDMIAGPSEVLILADDSAEPAFIAADMLAQAEH--DPQAAALLITTSAEVGKEVGKELES 291 Query: 649 QALQLPRVDIVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAG 707 Q QL R +I R + H I+L D ++A+ ++N+ A EHL LQI + ++ + +AG Sbjct: 292 QLEQLSRAEIARTALRDHGAILLVDSLDQAVALANEIAIEHLELQIRDPWAWLPKIRHAG 351 Query: 708 SVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRA 767 ++F+G++TPE+ GDY +G NH LPT G AR S TF K + + + + L+ Sbjct: 352 AIFLGSHTPEAAGDYVAGPNHVLPTMGTARISSALGVETFLKKSSIISYSAQALQQDAEH 411 Query: 768 VMCVAKKEGLDGHRNAVKIRMSK 790 + +A EGL H N+V IR+ + Sbjct: 412 IQRLAALEGLTAHGNSVAIRVKR 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: 663 Number of extensions: 33 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: 436 Length adjustment: 37 Effective length of query: 762 Effective length of database: 399 Effective search space: 304038 Effective search space used: 304038 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