Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_012171673.1 AZC_RS16245 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000010525.1:WP_012171673.1 Length = 430 Score = 258 bits (660), Expect = 4e-73 Identities = 166/434 (38%), Positives = 235/434 (54%), Gaps = 11/434 (2%) Query: 356 PIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKL 415 PI LD + L+ + ++++ V II VR +G++AL++Y+ FD V+L Sbjct: 2 PIRLDAKSTAFPDAFATFLASKREASTDVAVAVADIIAGVRARGDAALIDYSRTFDRVEL 61 Query: 416 SNPV-LNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFP 474 + + E + ++ EAL + + HA QLP + + L R+ Sbjct: 62 EGRIRVTEAEIEAALAEVPQDTFEALKFAKARIEAHHARQLPADERYTDAVGVELGQRWT 121 Query: 475 RPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKV 534 P++ VGLY+PGGTA PS+ LM VPA+VA + P DG ++P V+ A Sbjct: 122 -PVDAVGLYVPGGTAAYPSSVLMNAVPAKVAGVPRVAMVVP--SPDGVIAPLVLAAARLA 178 Query: 535 GASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAG 594 G ++ GGAQAVAA+AYGTETI VDKI+GPGN +V AAK V IDM AG Sbjct: 179 GVDEVYRVGGAQAVAALAYGTETIAPVDKIVGPGNAYVAAAKRQVFGKV----GIDMIAG 234 Query: 595 PSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLP 654 PSEVL++AD +A+ ++A+DLL+QAEH +Q ILV S + AV Q LP Sbjct: 235 PSEVLILADGNANAAWIAADLLAQAEHDAAAQSILV--TDSPVLADAVTRAVEAQLTTLP 292 Query: 655 RVDIVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGA 713 R +I H I+L +EAL + ++ APEHL + +A+ + +AG++FVGA Sbjct: 293 RREIAEASWRDHGAIILVGSMDEALPLVDRVAPEHLEIHADDADALADRIRHAGAIFVGA 352 Query: 714 YTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAK 773 YTPE+ GDY GTNH LPT AR SG F K + +P L IG A + +A+ Sbjct: 353 YTPEAIGDYVGGTNHVLPTARSARFSSGLGVYDFLKRTSILKCSPASLNVIGPAAVRLAE 412 Query: 774 KEGLDGHRNAVKIR 787 E LD H ++ IR Sbjct: 413 VERLDAHGRSILIR 426 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: 681 Number of extensions: 22 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: 430 Length adjustment: 37 Effective length of query: 762 Effective length of database: 393 Effective search space: 299466 Effective search space used: 299466 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 25 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