Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 206223 DVU0796 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >MicrobesOnline__882:206223 Length = 436 Score = 232 bits (592), Expect = 3e-65 Identities = 157/412 (38%), Positives = 225/412 (54%), Gaps = 18/412 (4%) Query: 387 LVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMKEALDL---S 443 +V I+ VR KG+ AL EYT +FD + +L+ EE + + + + + + Sbjct: 34 VVRDILAAVRSKGDEALAEYTRRFDCPDFTPALLHVT-SEEVAQAVASVPADDIAIIRQA 92 Query: 444 IENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTA---ILPSTALMLGV 500 +N+R FH AQ V G + + P+++ GLY+PGG L S+ LM + Sbjct: 93 ADNIRSFHEAQKERSWF-VTHDDGTILGQKVTPVDRAGLYVPGGKGGDTPLLSSLLMNAI 151 Query: 501 PAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPK 560 PAQVA I ASPPR DG ++P ++ A +G + I+ AG A AVAA A+GT+TI Sbjct: 152 PAQVAGVTSITVASPPRP-DGTLNPHLLAAAHILGITDIIRAGSAWAVAAFAFGTQTIAP 210 Query: 561 VDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAE 620 VD I GPGN FVT AK VQ +IDM AGPSE+L++AD A D+VA+D+LSQAE Sbjct: 211 VDVIAGPGNIFVTTAKRMVQGRV----AIDMIAGPSEILILADATARPDWVAADMLSQAE 266 Query: 621 HGIDSQVILVGVNLSEKKIQEIQDA-VHNQALQLPRVDIVRKCIAH-STIVLCDGYEEAL 678 H + ILV +E + E A + Q LPR DI RK +A +V+ + A+ Sbjct: 267 HDPLASSILV---TTEPALAEAVTAELERQLATLPRADIARKALADWGAVVVVPDMDVAV 323 Query: 679 EMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQ 738 ++N+ APEHL + A + + +AG++F+G Y+PE GDY +G NH LPT G AR Sbjct: 324 AIANRVAPEHLEVLTAQPWELAGSLRHAGALFLGPYSPEPLGDYFAGPNHVLPTMGTARF 383 Query: 739 YSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSK 790 S + TF K + + E AV +A+ EGL+ H + R S+ Sbjct: 384 SSALSVQTFCKRTSIIAASRAFAERNADAVARLARLEGLEAHARSAASRNSQ 435 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: 636 Number of extensions: 31 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: 436 Length adjustment: 37 Effective length of query: 762 Effective length of database: 399 Effective search space: 304038 Effective search space used: 304038 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