Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_012676228.1 PERMA_RS09180 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000021565.1:WP_012676228.1 Length = 429 Score = 262 bits (669), Expect = 3e-74 Identities = 166/421 (39%), Positives = 244/421 (57%), Gaps = 19/421 (4%) Query: 372 KALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP---VLNAPFPEEY 428 K + R + + V II+NV++KG+ AL++YTE FD VKLS+P V+ E+ Sbjct: 19 KLIKRSEMEIEQYETAVKDIIKNVKEKGDEALIDYTELFDKVKLSSPEELVITFDELEKA 78 Query: 429 FEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGT 488 ++ L ++ K AL++++E V+ FH AQ+ L E G+L + P+E+VGLY+PGG Sbjct: 79 YDQLDDDTKWALEVALERVKSFHEAQIERSYLLEEE--GMLLGQKVIPMERVGLYVPGGK 136 Query: 489 AILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAV 548 A PST +M PA+VA KE+V SP + K + ++ G + GGAQA+ Sbjct: 137 AAYPSTVIMNAAPAKVAGVKEMVMCSP---NPNKYTLAAAFLC---GVDTVYRIGGAQAI 190 Query: 549 AAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADV 608 AAMAYGTET+ KVDKI+GPGN FV AK V + ID AGPSE+LVIADE A+ Sbjct: 191 AAMAYGTETVKKVDKIVGPGNIFVALAKKNVYG----IVDIDSIAGPSEILVIADETANP 246 Query: 609 DFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQ-LPRVDIVRKCIA-HS 666 ++VA+DLLSQAEH D + V SE ++++ ++N L+ R +I RK + + Sbjct: 247 EWVAADLLSQAEH--DELAASILVTTSEDLAIDVKNILYNVLLKDFEREEIARKSLDNYG 304 Query: 667 TIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGT 726 I + D + A E+SN APEHL + + D ++ + +AG++F+G Y+ E GDY G Sbjct: 305 HIFIVDDLDTACEVSNFIAPEHLEIITKSPFDLLEKIKHAGAIFLGEYSTEPLGDYILGP 364 Query: 727 NHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKI 786 NH LPT AR S F K + ++ EG + + + +A EGL HR +V++ Sbjct: 365 NHVLPTGRSARFSSPLGVYDFIKRSSIIYVSREGFDRVEKYARQIATAEGLYAHRLSVEV 424 Query: 787 R 787 R Sbjct: 425 R 425 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: 770 Number of extensions: 45 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: 429 Length adjustment: 36 Effective length of query: 763 Effective length of database: 393 Effective search space: 299859 Effective search space used: 299859 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