Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_015738354.1 ADEG_RS01575 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000024605.1:WP_015738354.1 Length = 425 Score = 272 bits (696), Expect = 2e-77 Identities = 165/424 (38%), Positives = 237/424 (55%), Gaps = 10/424 (2%) Query: 366 DKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFP 425 D + + L R SE V I++ V++KG+ A+L +T +FD V L L Sbjct: 8 DDPRLPQVLDRRFSFPSEAADQVASILQEVKEKGDEAVLSFTARFDRVNLRPEELEVTAA 67 Query: 426 E--EYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLY 483 E +E ++ A+ ++ + FHA +P EV+ G + RP+E+VG+Y Sbjct: 68 EIDRAYEEVSPAYLTAVKCAVTRIFNFHAKHVPKSWHEVKPD-GSVWGELVRPLERVGIY 126 Query: 484 IPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAG 543 +PGG A PS+ LM VPA+VA KEIV A+PP +G+V P V+ A + G S+I G Sbjct: 127 VPGGRARYPSSVLMNAVPARVAGVKEIVMATPPGP-EGRVDPHVLVAAREAGVSRIFRVG 185 Query: 544 GAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIAD 603 GAQAVAA+AYGTE IP+VDKI+GPGN +VT AK V ID+ AGPSEV V+AD Sbjct: 186 GAQAVAALAYGTERIPRVDKIVGPGNIYVTLAKRMVFGQV----GIDLLAGPSEVAVVAD 241 Query: 604 EDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI 663 E A +VA+DLL+QAEH ++V+LV S + +E+ + + L R+ + Sbjct: 242 ETAPAAWVAADLLAQAEHDPQARVLLV--TTSRELAEEVNRRLQEEWRSLGSPSGAREAL 299 Query: 664 AHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYS 723 S VL AL+ N++APEHL L +A+ V+ V +AG++F+G Y+P GDY Sbjct: 300 LASWAVLVPDLSAALDCVNRFAPEHLELLVADPAPLVEQVKHAGAIFLGPYSPVPMGDYI 359 Query: 724 SGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNA 783 +G NH LPT G AR S A F K + ++P + + +A+ EGL H A Sbjct: 360 AGPNHVLPTGGTARFASPLGVADFLKRTSVLKLSPAAFQELAPHAAALAEVEGLVAHARA 419 Query: 784 VKIR 787 +K+R Sbjct: 420 IKVR 423 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: 683 Number of extensions: 31 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: 425 Length adjustment: 36 Effective length of query: 763 Effective length of database: 389 Effective search space: 296807 Effective search space used: 296807 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