Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_018947394.1 B1A74_RS12400 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_001995255.1:WP_018947394.1 Length = 434 Score = 237 bits (605), Expect = 9e-67 Identities = 145/406 (35%), Positives = 228/406 (56%), Gaps = 16/406 (3%) Query: 388 VNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEM----KEALDLS 443 V I++ V+ +G++A+L YTE+FD ++ + V P++ + E + +EAL+ + Sbjct: 36 VREILDAVKAEGDAAVLRYTERFDRLERDS-VAGLEVPQQRLQAALEAIPAAQREALETA 94 Query: 444 IENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQ 503 E + ++ Q + + VL R P++ VGLY+PGG A PS+ LM VPA+ Sbjct: 95 AERIGEYARHQSMQDWQFTDADGTVLGQRVT-PLDSVGLYVPGGKAAYPSSVLMNAVPAR 153 Query: 504 VAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDK 563 VA +++ P DG+++ V+ A G ++ GGAQAV A+AYGT TIP VDK Sbjct: 154 VAGVGQLIMVVPA--PDGELNDLVLAAAAVAGVDRVFTVGGAQAVGALAYGTATIPAVDK 211 Query: 564 ILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGI 623 I+GPGN FV AAK + IDM AGPSE+LV+ D + D +++A+DL SQAEH Sbjct: 212 IVGPGNIFVAAAK----REVFGTVGIDMIAGPSEILVVCDGETDPEWIAADLFSQAEHDE 267 Query: 624 DSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYEEALEMSN 682 +Q IL V+ + + +A+ ++PR DI+R + + ++ ++A+ ++N Sbjct: 268 QAQSIL--VSWDHAFLDRVNEAMDRLLEEMPRADIIRTSLQNRGALIAARDLDDAVAVAN 325 Query: 683 QYAPEHLILQIANANDYVKL-VDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSG 741 + APEHL L +A+ + + +AG+VF+G +T E+ GDY +G NH LPT AR S Sbjct: 326 RVAPEHLELSLADPQAALDAGLRHAGAVFMGRHTSEALGDYCAGPNHVLPTSRTARFSSP 385 Query: 742 ANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787 FQK + +PEG +GR +A EGL H + ++R Sbjct: 386 LGVYDFQKRSSIIQCSPEGAARLGRTAAELAHGEGLTAHARSAELR 431 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: 659 Number of extensions: 29 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: 434 Length adjustment: 37 Effective length of query: 762 Effective length of database: 397 Effective search space: 302514 Effective search space used: 302514 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