Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_048060775.1 MTH_RS01020 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000008645.1:WP_048060775.1 Length = 424 Score = 321 bits (823), Expect = 4e-92 Identities = 183/420 (43%), Positives = 257/420 (61%), Gaps = 9/420 (2%) Query: 370 VQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429 + + + R +++ V II VRD G+ AL E T +FDGV + N ++ EE Sbjct: 11 ISELVERARLDVDDVLGPVADIISMVRDGGDDALRELTGRFDGVTVENFRVSREEIEEAH 70 Query: 430 EGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTA 489 + L +KEAL + N+ +FH Q+P+ + E +PGV+ + RPI+ VG YIPGG A Sbjct: 71 KNLEPGVKEALREAASNIEEFHRMQMPSGWMS-EVRPGVMAGQLVRPIDSVGCYIPGGRA 129 Query: 490 ILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVA 549 + PST LM +PA++A + IV +PP + DG V V+ A+ GAS+I GGAQAVA Sbjct: 130 VYPSTILMTVIPARIAGVERIVCCTPPAQ-DGSVPDAVLVAADMAGASEIYRVGGAQAVA 188 Query: 550 AMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVD 609 AMAYGTETI VDKI+GPGN FVTAAK V + ID PAGPSEVL+IADE A + Sbjct: 189 AMAYGTETIRPVDKIVGPGNIFVTAAKKLVYGEVD----IDFPAGPSEVLIIADETASPE 244 Query: 610 FVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTI 668 ++A ++L+QAEH D Q V V S E+++ VH + R +I+R+ + + I Sbjct: 245 YIALEILAQAEH--DPQAASVLVTDSRDLALEVKEMVHENIKYMERANIIRESLERYGMI 302 Query: 669 VLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNH 728 VL +EA++ SN YAPEHL++ + + ++ + NAGS+F+G +P + GDY SGTNH Sbjct: 303 VLTADIDEAVDFSNAYAPEHLVIMTDSPEETLEGIRNAGSIFLGELSPVAAGDYGSGTNH 362 Query: 729 TLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 LPT G AR YSG +T +F K T Q IT EGL N+ V+ +A+ EGL H + + R+ Sbjct: 363 VLPTSGCARMYSGLSTESFIKKPTVQRITKEGLRNLQGTVLKLAEYEGLHAHAESFRRRL 422 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: 662 Number of extensions: 35 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 799 Length of database: 424 Length adjustment: 36 Effective length of query: 763 Effective length of database: 388 Effective search space: 296044 Effective search space used: 296044 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