Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_020564986.1 A3OW_RS0118680 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000372865.1:WP_020564986.1 Length = 434 Score = 235 bits (600), Expect = 3e-66 Identities = 142/409 (34%), Positives = 222/409 (54%), Gaps = 13/409 (3%) Query: 383 EIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP-VLNAPFP--EEYFEGLTEEMKEA 439 ++ V I+ ++R +G+ AL+EYT +FD +++ L P ++ ++GL ++ +A Sbjct: 33 DVHRRVIDILADIRSRGDQALVEYTNRFDRRQITQAGELEMPKAVLKQAWDGLPQDQAKA 92 Query: 440 LDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLG 499 L + + +R + A + E G + + P+++VGLY+PGG A PS+ LM Sbjct: 93 LQTAADRIRAY-AEHQKMASWEFTEADGTVLGQKITPLDRVGLYVPGGKAAYPSSVLMNA 151 Query: 500 VPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIP 559 +PA+VA E++ P G+ + V+ A G ++ GGAQAVAA+AYGT TIP Sbjct: 152 IPAKVAGVAELIMVVPT--PGGEANSMVLAAAWLAGVDRVFTVGGAQAVAALAYGTGTIP 209 Query: 560 KVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQA 619 V KI+GPGN +V AK V IDM AGPSE+L+I D D D++A DL SQA Sbjct: 210 PVAKIVGPGNIYVATAKKLVFGQV----GIDMIAGPSEILIICDGKTDPDWIAMDLFSQA 265 Query: 620 EHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYEEAL 678 EH ++Q IL+ + + ++ ++ + R DI+R + ++ D A Sbjct: 266 EHDENAQAILISDDPGF--LDAVEASIRRLLPTMERADIIRASLTERGALIRVDHLLVAA 323 Query: 679 EMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQ 738 ++N+ APEHL L +A + + +AG++F+G YT E+ GDY +G NH LPT G AR Sbjct: 324 SVANRIAPEHLELSVAEPEALSRHIRHAGAIFMGRYTAEALGDYCAGPNHVLPTSGTARF 383 Query: 739 YSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787 S FQK + N +P G +GRA +A+ E L H + + R Sbjct: 384 SSPLGVYDFQKRTSLINCSPAGARTLGRAASILARGEQLTAHARSAEYR 432 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: 702 Number of extensions: 35 Number of successful extensions: 5 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 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