Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_028988607.1 G579_RS0100400 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000423825.1:WP_028988607.1 Length = 432 Score = 251 bits (640), Expect = 8e-71 Identities = 154/406 (37%), Positives = 228/406 (56%), Gaps = 15/406 (3%) Query: 388 VNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPE----EYFEGLTEEMKEALDLS 443 V ++ VR++G+ A+L+YT++FD ++ +N + P E GL +EAL L+ Sbjct: 33 VRDVLHAVREQGDRAVLDYTQRFDRLR-ANSLAELEVPRAKLREALAGLAPADREALALA 91 Query: 444 IENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQ 503 E +R +H Q+ E+ E G + P+ +VG+Y+PGG A PS+ LM +PA+ Sbjct: 92 AERIRSYHERQV-AESWEYSEADGTRLGQRVTPLARVGIYVPGGKAAYPSSVLMNAIPAK 150 Query: 504 VAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDK 563 VA EI+ P G+++P V+ AE G ++ GGAQAVAA+AYGTET+P VDK Sbjct: 151 VAGVAEIIMVVPA--PGGELNPLVLAAAELAGVDRVFTIGGAQAVAALAYGTETVPAVDK 208 Query: 564 ILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGI 623 I+GPGN +V AK V IDM AGPSE+LVI+D D D++A DLLSQAEH Sbjct: 209 IVGPGNIYVATAKRMVFGRV----GIDMIAGPSEILVISDGQTDPDWLAMDLLSQAEHDE 264 Query: 624 DSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI-AHSTIVLCDGYEEALEMSN 682 +Q IL+ + + + +V L R I R+ + + ++L EA +++ Sbjct: 265 QAQSILISWDAD--CLTRVAASVDKLLPTLEREAIARQAWDSRAALILVRDAAEACAVAD 322 Query: 683 QYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGA 742 + APEHL L +A+ + + + NAG+VF+G YT E+ GDY +G NH LPT G AR S Sbjct: 323 RIAPEHLELSVADPDALLPALHNAGAVFMGRYTAEALGDYVAGPNHVLPTAGSARFSSPL 382 Query: 743 NTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 FQK + + G + +GRA +A+ EGL H + R+ Sbjct: 383 GVYDFQKRTSIIYASAVGADQLGRAAKRLAEGEGLTAHARSAAYRI 428 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: 660 Number of extensions: 33 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: 432 Length adjustment: 37 Effective length of query: 762 Effective length of database: 395 Effective search space: 300990 Effective search space used: 300990 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