Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_013722206.1 ALIDE2_RS12495 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000204645.1:WP_013722206.1 Length = 439 Score = 207 bits (528), Expect = 7e-58 Identities = 143/424 (33%), Positives = 217/424 (51%), Gaps = 11/424 (2%) Query: 372 KALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEG 431 KA+ ++ +++ V II+++ +G+ A+ EY+ KFD ++ L+ + + Sbjct: 9 KAMQVRAEEDAKVRATVECIIKDIELRGDEAVREYSRKFDQWDPADFRLSQAEIDAARKS 68 Query: 432 LTEEMKEALDLSIENVRKFHAAQLPT-ETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAI 490 L+ E + + + VR F Q + + +EV+T PGV+ P+ VG YIPGG Sbjct: 69 LSAREIEDIAFAQKQVRNFAQIQRDSMKDVEVQTHPGVILGHKHLPVNAVGCYIPGGKYP 128 Query: 491 LPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAA 550 L ++A M + A+VA + +V +PP + GK P +V GA +I++ GG QAV A Sbjct: 129 LLASAHMSVLTAKVAGVRRVVSTAPPFQ--GKPHPAIVTAMHMAGADEILVLGGVQAVVA 186 Query: 551 MAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDF 610 MA GT++I VD ++GPGN FV AK + ID+ AGP+E LVIADE D + Sbjct: 187 MAVGTQSIAPVDMLVGPGNMFVAEAKRQLFGRV----GIDLFAGPTETLVIADESVDAEM 242 Query: 611 VASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIV 669 A DLL QAEHG S +L + SEK +E V Q LP I + A + ++ Sbjct: 243 CAVDLLGQAEHGPTSPAVL--LTTSEKLAKETMAEVERQLRILPTAAIAAQSWAEYGEVI 300 Query: 670 LCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHT 729 +CD E LE ++ A EH+ + + + ++ + N G++F+G T S GD GTNHT Sbjct: 301 VCDSDAEMLEKADALASEHVQVMTRDPDYFLNRLSNYGALFLGPRTNVSFGDKVIGTNHT 360 Query: 730 LPTYGYARQYSGANTATFQKFITAQNI-TPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 LPT AR G F K T Q + T E +G + E GH +R+ Sbjct: 361 LPTNKAARYTGGLWVGKFLKTCTYQKVLTDEASALMGEYCSRLCHMENFVGHGEQANLRV 420 Query: 789 SKLG 792 + G Sbjct: 421 RRYG 424 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: 725 Number of extensions: 33 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: 439 Length adjustment: 37 Effective length of query: 762 Effective length of database: 402 Effective search space: 306324 Effective search space used: 306324 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