Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_011940838.1 GURA_RS20635 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000016745.1:WP_011940838.1 Length = 429 Score = 252 bits (643), Expect = 3e-71 Identities = 158/435 (36%), Positives = 239/435 (54%), Gaps = 15/435 (3%) Query: 359 LDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSN- 417 LD+ + + L+R + E+ +V II VR +G++ALL+YT +FD ++ Sbjct: 4 LDIHDNNFEANFAAILARGEETGKEVEQVVLDIIAAVRKEGDAALLDYTRRFDRLEADTV 63 Query: 418 ---PVLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFP 474 V A F E + ++ AL L++E V +FH Q L + + VL + Sbjct: 64 ADLEVTEAEFNEAFVRVADADIS-ALKLAVERVARFHEKQKQETWLSTD-ESDVLLGQMV 121 Query: 475 RPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKV 534 P+E+VG+Y+PGG A PS+ +M VPA+VA E+V +P G+++ V+ A Sbjct: 122 TPLERVGIYVPGGKASYPSSVIMNAVPAKVAGVGEVVMVAPT--PGGEINHHVLVAARLS 179 Query: 535 GASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAG 594 G ++ GGAQAVAA+AYGT +P+VDKI GPGN +V AK V IDM AG Sbjct: 180 GVDRVFRIGGAQAVAALAYGTAMVPRVDKITGPGNIYVATAKKLVFGQV----GIDMIAG 235 Query: 595 PSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLP 654 PSE+LVI D + +A+DLLSQAEH + IL+ + S + + V Q +L Sbjct: 236 PSEILVINDGSGNPAHIAADLLSQAEHDELASSILITTSRSFG--ERVAAEVELQLGKLK 293 Query: 655 RVDIVRKCI-AHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGA 713 R I RK + +++ EA+ SN+ APEHL L + + + + NAG++F+G Sbjct: 294 RESIARKSWDTYGAVIVAGSIAEAIAFSNRIAPEHLELAVTDPFAILPQIRNAGAIFLGH 353 Query: 714 YTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAK 773 +TPE+ GDY +G NHTLPT G AR +S + F K + + GL +G+ ++ +A+ Sbjct: 354 FTPEAAGDYLAGPNHTLPTGGTARFFSPLSVDDFIKKSSIVYFSESGLNRLGKDIVRIAE 413 Query: 774 KEGLDGHRNAVKIRM 788 EGL+ H +V IR+ Sbjct: 414 LEGLEAHGKSVSIRL 428 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: 649 Number of extensions: 21 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: 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