Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_085772742.1 B1812_RS17550 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_002117405.1:WP_085772742.1 Length = 433 Score = 253 bits (645), Expect = 2e-71 Identities = 167/434 (38%), Positives = 238/434 (54%), Gaps = 18/434 (4%) Query: 363 KASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNA 422 K S +G ++ L+ + T V II++V +G++AL++Y+ +FD + L + Sbjct: 15 KFSALLGQKRDLAPDVDAT------VKAIIDDVVARGDAALVDYSRRFDRIDLEKSGIAV 68 Query: 423 PFPE-EYFEG-LTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKV 480 E EG ++E +ALDL++E + FH Q P + L GV PI+ V Sbjct: 69 SKAEIASAEGRCSKEQLDALDLALERILVFHEKQRPQD-LRFTDPLGVELGWRWTPIDSV 127 Query: 481 GLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIV 540 GLY+PGGTA PS+ LM PA+VA I P G+V+P V+ A++ G +I Sbjct: 128 GLYVPGGTAAYPSSVLMNVAPAKVAGVSRIAMVVPT--PGGEVAPLVLAAAKRAGIEEIY 185 Query: 541 LAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLV 600 GGAQAVAA+AYGT+TI VDKI+GPGN +V AAK V IDM AGPSEVL+ Sbjct: 186 RVGGAQAVAALAYGTKTIAPVDKIVGPGNAYVAAAKRRVFGQV----GIDMIAGPSEVLI 241 Query: 601 IADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVR 660 +AD A+ D++A+DLL+QAEH +Q IL+ + S + AV L R +I Sbjct: 242 LADSSANPDWIAADLLAQAEHDESAQSILITDDAS--LADAVVAAVERHLKTLTRHEIAS 299 Query: 661 KCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESC 719 + ++L +AL ++++ A EHL L +A + NAG++FVG YTPE+ Sbjct: 300 ASWRDYGAVILVRSLADALPLADRIAAEHLELVCEDAEALAAKIKNAGAIFVGGYTPEAI 359 Query: 720 GDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDG 779 GDY G+NH LPT AR SG N F K + E L IG A + + + EGL Sbjct: 360 GDYVGGSNHVLPTARSARFSSGLNVLDFLKRSSILKCDAEALRAIGGAAVTLGEAEGLTA 419 Query: 780 HRNAVKIRMSKLGL 793 H +V IR++ LG+ Sbjct: 420 HARSVSIRLNSLGV 433 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: 642 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: 433 Length adjustment: 37 Effective length of query: 762 Effective length of database: 396 Effective search space: 301752 Effective search space used: 301752 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