Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_106717792.1 CU100_RS17230 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_003010935.1:WP_106717792.1 Length = 434 Score = 215 bits (547), Expect = 5e-60 Identities = 144/418 (34%), Positives = 216/418 (51%), Gaps = 11/418 (2%) Query: 378 IQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMK 437 I + + + V ++ V G+ A+ + +FDG+ + L + + LT + + Sbjct: 14 ISQDALLTKAVESLLTQVEKGGDEAVHALSVRFDGLDRRSYRLTDAEIKNCVDNLTRQQR 73 Query: 438 EALDLSIENVRKFHAAQLPT-ETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTAL 496 +D + + VR F AQ +EVET PGV+ PI VG Y+PGG L ++A Sbjct: 74 ADIDFAQDQVRNFAQAQKNALRDIEVETLPGVVLGHKNVPIANVGCYVPGGKYPLLASAH 133 Query: 497 MLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTE 556 M + A+VA C+ ++ +PP +G+++P +V GA +I GG QA+AAMA GTE Sbjct: 134 MSVLTAKVAGCERVITCAPP--FNGEIAPLIVAAQHLAGADEIYCLGGVQAIAAMALGTE 191 Query: 557 TIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLL 616 TI VD + GPGN +V AK + ID+ AGP+E LVIADE D + A+DLL Sbjct: 192 TIDAVDMLAGPGNAYVAEAKRLLFGRV----GIDLFAGPTETLVIADETVDGEICATDLL 247 Query: 617 SQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYE 675 QAEHG++S +L + SEK ++ + LP +I RK I++CD E Sbjct: 248 GQAEHGVNSPAVL--ITNSEKLARDTLREIDRLLEILPTREIARKAWEDCGEIIVCDTLE 305 Query: 676 EALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGY 735 E +E++++ A EH+ + + ++ + N G++F+G T + GD GTNHTLPT Sbjct: 306 EMVEVADRIASEHVQVMTRDPQYFLDRMKNYGALFLGQRTTVAYGDKVIGTNHTLPTKRA 365 Query: 736 ARQYSGANTATFQKFITAQNI-TPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKLG 792 AR G F K T Q I T E IG ++ EG GH IR+ + G Sbjct: 366 ARYTGGLWVGKFIKTCTYQKIVTDEASVLIGEYCSRLSIMEGFAGHAEQANIRVRRYG 423 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: 710 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 Jul 26 2024. The underlying query database was built on Jul 25 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