Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_011800110.1 PNAP_RS03445 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000015505.1:WP_011800110.1 Length = 447 Score = 254 bits (648), Expect = 9e-72 Identities = 160/441 (36%), Positives = 238/441 (53%), Gaps = 16/441 (3%) Query: 356 PIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKL 415 P L + A+ + + L + I V I+ +V+ +G++A+L+YT +FDG+ Sbjct: 7 PARLSCLDATFEAQFKARLHWSADTDAHIEQRVADILADVQQRGDAAVLDYTARFDGLNA 66 Query: 416 SNPV---LNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPT--ETLEVETQPGVLC 470 ++ L + FE + +EAL + VR +H AQ E+ + G L Sbjct: 67 ASMAELELTQAELKAAFESIPAAQREALQAAARRVRTYHEAQKKASGESWSYRDEDGTLL 126 Query: 471 SRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASP-PRKSDGKVSPEVVY 529 + P+++VG+Y+PGG A PS+ LM +PA VA EI+ P PR + Y Sbjct: 127 GQKVTPLDRVGIYVPGGKAAYPSSVLMNAIPAHVAGVGEIIMVVPTPRGEKNALVLAAAY 186 Query: 530 VAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSI 589 VA G ++ GGAQAVAA+AYGT T+PKVDKI GPGN +V +AK V I Sbjct: 187 VA---GVTRAFTIGGAQAVAALAYGTATVPKVDKITGPGNAYVASAKKRVFGTV----GI 239 Query: 590 DMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQ 649 DM AGPSE+LV+AD D+VA DL SQAEH +Q IL+ + + I +Q+A++ Sbjct: 240 DMIAGPSEILVLADGTTPADWVAMDLFSQAEHDELAQSILLCPDAAY--IDAVQEAINRL 297 Query: 650 ALQLPRVDIVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGS 708 +PR I+ K ++ ++ EEA E+SN+ APEHL + + + L+ +AG+ Sbjct: 298 LPAMPRAGIIAKSLSDRGALIHTRSMEEACEISNRIAPEHLEVSSREPHRWEPLLRHAGA 357 Query: 709 VFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAV 768 +F+GAYT ES GDY +G NH LPT G AR S FQK + ++ G + +G Sbjct: 358 IFLGAYTSESLGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSLIEVSEAGAQILGPIA 417 Query: 769 MCVAKKEGLDGHRNAVKIRMS 789 +A EGL H A ++R++ Sbjct: 418 AELAYGEGLQAHARAAELRLA 438 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: 673 Number of extensions: 37 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 09 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