Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_106715409.1 CU100_RS05115 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_003010935.1:WP_106715409.1 Length = 430 Score = 256 bits (655), Expect = 1e-72 Identities = 162/414 (39%), Positives = 233/414 (56%), Gaps = 12/414 (2%) Query: 379 QKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP--VLNAPFPEEYFEGLTEEM 436 + + ++ +V II VR +G+SAL++Y+++FD V L + + + + Sbjct: 25 EASEDVDRVVTDIIHRVRTEGDSALIDYSQRFDRVDLVQHGIAITSAEIDAAVASAPAKT 84 Query: 437 KEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTAL 496 EAL L+ + HA Q+P + + L SR+ +E VGLY+PGGTA PS+ L Sbjct: 85 VEALKLARNRIHSHHARQMPQDDRYTDALGVELGSRWTA-VESVGLYVPGGTASYPSSVL 143 Query: 497 MLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTE 556 M VPAQVA + IV P DGK++P V+ A G S+I GGAQA+AA+AYGTE Sbjct: 144 MNAVPAQVAGVERIVMVVP--SPDGKLNPLVLVAARLAGVSEIYRVGGAQAIAALAYGTE 201 Query: 557 TIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLL 616 TI V KI+GPGN +V AAK V IDM AGPSEVL++AD + D D++A+DLL Sbjct: 202 TIAPVAKIIGPGNAYVAAAKRRVFGRV----GIDMIAGPSEVLIVADSNNDPDWIAADLL 257 Query: 617 SQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYE 675 +QAEH +Q IL+ + E + AV Q L LPR + R + + ++L Sbjct: 258 AQAEHDSAAQSILITDD--ESFGDAVVAAVERQLLTLPRAEAARASWSDYGAVILVSDLL 315 Query: 676 EALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGY 735 +L + N+ A EHL + + + V NAG++F+G YTPE GDY G+NH LPT Sbjct: 316 SSLPLVNRIAAEHLEIATDDPELLMAGVRNAGAIFLGRYTPEVIGDYVGGSNHVLPTARS 375 Query: 736 ARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789 AR SG + + K + + E L +G A + +A+ EGLD H N+V IR++ Sbjct: 376 ARFSSGLSVLDYVKRTSILKLGVEQLRALGPAAIELARAEGLDAHGNSVAIRLN 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: 634 Number of extensions: 26 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