Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_068174408.1 HTA01S_RS19435 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_001592305.1:WP_068174408.1 Length = 447 Score = 260 bits (665), Expect = 1e-73 Identities = 163/442 (36%), Positives = 239/442 (54%), Gaps = 14/442 (3%) Query: 356 PIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKL 415 P+ L + + L + S I V I+ +V+ +G++A+LEYT +FDG+ Sbjct: 7 PVRLSTQSSDFEARFAARLHWSAETDSAIEQRVADILADVQQRGDAAVLEYTARFDGLNA 66 Query: 416 SN-PVLNAPFPE--EYFEGLTEEMKEALDLSIENVRKFHAAQLPT--ETLEVETQPGVLC 470 P L E F+GL ++AL+ + VR +H AQ E+ + G L Sbjct: 67 DGVPALELTQAELKAAFDGLPAAQRDALESAARRVRSYHEAQKRASGESWSYRDEDGTLL 126 Query: 471 SRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYV 530 + P+++VG+Y+PGG A PS+ LM +PA VA EI+ P K G+ +P V+ Sbjct: 127 GQKVTPLDRVGIYVPGGKAAYPSSVLMNAIPAHVAGVAEIIMVVPTPK--GEKNPLVLAA 184 Query: 531 AEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSID 590 A G ++ GGAQAVAA+AYGT T+PKVDKI GPGN +V +AK V ID Sbjct: 185 AYVAGVTRAFTIGGAQAVAALAYGTATVPKVDKITGPGNAYVASAKKRVFGTV----GID 240 Query: 591 MPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQA 650 M AGPSE+LV+AD D+VA DL SQAEH +Q IL+ + + I +Q A+ Sbjct: 241 MIAGPSEILVLADGSTPADWVAMDLFSQAEHDELAQSILLCPDAAY--IDAVQAAIDRLL 298 Query: 651 LQLPRVDIVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSV 709 +PR I+ K + ++L EEA +SN+ APEHL + + + + L+ +AG++ Sbjct: 299 PTMPRAAIIAKSLNDRGALILTRDMEEACAISNRIAPEHLEVSSSEPHRWEPLLKHAGAI 358 Query: 710 FVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVM 769 F+GAYT ES GDY +G NH LPT G AR S FQK + ++ G + +G Sbjct: 359 FLGAYTSESLGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSLIEVSAAGAQTLGIIAA 418 Query: 770 CVAKKEGLDGHRNAVKIRMSKL 791 +A EGL H A ++R++ + Sbjct: 419 ELAYGEGLQAHARAAELRLTNV 440 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: 694 Number of extensions: 29 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: 447 Length adjustment: 37 Effective length of query: 762 Effective length of database: 410 Effective search space: 312420 Effective search space used: 312420 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