Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_106709380.1 CU102_RS02655 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_003010955.1:WP_106709380.1 Length = 430 Score = 249 bits (636), Expect = 2e-70 Identities = 162/413 (39%), Positives = 227/413 (54%), Gaps = 14/413 (3%) Query: 381 TSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMK--- 437 + ++ V II VR +G+ AL++Y++ FD V L + A P E + Sbjct: 27 SEDVDRAVADIIHRVRSEGDKALIDYSKAFDRVDLVQHGI-AITPAEIDAAVASAPAATV 85 Query: 438 EALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALM 497 EAL L+ + + HA Q+P + + GV +E VGLY+PGGTA PS+ LM Sbjct: 86 EALKLARDRIHSHHARQVPQDDRYTDAL-GVELGSHWTAVESVGLYVPGGTASYPSSVLM 144 Query: 498 LGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTET 557 VPAQVA + IV P DG+++P V+ A G S+I GGAQA+AA+AYGTET Sbjct: 145 NAVPAQVAGVERIVMVVP--SPDGRLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTET 202 Query: 558 IPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLS 617 I V KI+GPGN +V AAK V IDM AGPSEVL++AD D D D++A+DLL+ Sbjct: 203 IAPVAKIVGPGNAYVAAAKRRVFGTV----GIDMIAGPSEVLIVADSDNDPDWIAADLLA 258 Query: 618 QAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEE 676 QAEH +Q IL+ + E + AV Q LPR + ++L + Sbjct: 259 QAEHDSAAQSILITDD--EGFGNAVVSAVERQLQTLPRTATASASWRDYGAVILVQDLDA 316 Query: 677 ALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYA 736 +L + N+ A EHL + A+ + V NAG++F+G YTPE GDY G+NH LPT A Sbjct: 317 SLPLVNRIAAEHLEIATADPERLLAGVRNAGAIFLGRYTPEVIGDYVGGSNHVLPTARSA 376 Query: 737 RQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789 R SG + + K + + E L +G A + +A+ EGLD H N+V IR++ Sbjct: 377 RFSSGLSVLDYVKRTSILKLGVEQLRALGPAAIELARAEGLDAHGNSVAIRLN 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: 650 Number of extensions: 25 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: 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 26 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