Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_013517767.1 ALIDE2_RS04130 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000204645.1:WP_013517767.1 Length = 438 Score = 261 bits (668), Expect = 4e-74 Identities = 160/442 (36%), Positives = 241/442 (54%), Gaps = 14/442 (3%) Query: 353 LTGPIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDG 412 + P L V + + L + + I V I+ +V+ +G++A+L+YT +FDG Sbjct: 4 VAAPARLSTVSDAFEADFAARLHWSADQDAAIEERVAAILADVQQRGDAAVLDYTRRFDG 63 Query: 413 VKLSNPV---LNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPT--ETLEVETQPG 467 ++ L + ++GL + ++AL + VR +H AQ E+ + G Sbjct: 64 LQADGVAALELTQAELKAAYDGLPDAQRQALSAAAARVRSYHEAQKKACGESWSYRDEDG 123 Query: 468 VLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEV 527 L + P+++VG+Y+PGG A PS+ LM +PA VA EI+ P + G+ +P V Sbjct: 124 TLLGQKVTPLDRVGIYVPGGKAAYPSSVLMNAIPAHVAGVPEIIMVVPTPR--GEKNPLV 181 Query: 528 VYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALC 587 + A G ++ GGAQAVAA+A+GT TIPKVDKI GPGN +V +AK V Sbjct: 182 LAAACVAGVTRAFTIGGAQAVAALAHGTATIPKVDKITGPGNAYVASAKKRVFGQV---- 237 Query: 588 SIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVH 647 IDM AGPSE+LV+AD D+VA DL SQAEH +Q IL+ + + I +Q + Sbjct: 238 GIDMIAGPSEILVLADGSTPPDWVAMDLFSQAEHDELAQSILLCPDAAY--IDAVQREID 295 Query: 648 NQALQLPRVDIV-RKCIAHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNA 706 Q+PR +I+ R ++ EEA E+SN+ APEHL + + + + L+ +A Sbjct: 296 RLLPQMPRAEIIARSLTGRGALIHTRSMEEACEISNRIAPEHLEVSSRDPHKWEPLLRHA 355 Query: 707 GSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGR 766 G++F+GAYT ES GDY +G NH LPT G AR S FQK + ++ +G + +GR Sbjct: 356 GAIFLGAYTSESLGDYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSLIEVSEQGAQALGR 415 Query: 767 AVMCVAKKEGLDGHRNAVKIRM 788 +A EGL GH A ++R+ Sbjct: 416 IASVLAHGEGLQGHARAAEMRL 437 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: 705 Number of extensions: 34 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: 438 Length adjustment: 37 Effective length of query: 762 Effective length of database: 401 Effective search space: 305562 Effective search space used: 305562 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