Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_011840632.1 RSPH17029_RS04215 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000015985.1:WP_011840632.1 Length = 441 Score = 202 bits (514), Expect = 3e-56 Identities = 146/437 (33%), Positives = 206/437 (47%), Gaps = 18/437 (4%) Query: 357 IHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLS 416 ++ V+ D G L R S + V PI+E VR +G++AL+ + + D K Sbjct: 4 VNFQVLAELDAAGRAALLRRSETDLSMFLEKVGPILEAVRTEGDAALVRFGRELDRAKGL 63 Query: 417 N----PVLNAPFPEEYFEGLTE-EMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCS 471 V A F E + GL E E+ EA+ +I N+R FH Q P E +PG Sbjct: 64 TREGLKVTEAEFDEAF--GLVEPEIVEAIRFAIGNIRTFHEEQAPEPMWLKELRPGAFAG 121 Query: 472 RFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVA 531 PI V LY+P G PS +M VPA VA+ +I +PP DGKV + A Sbjct: 122 DRFTPIRSVALYVPRGKGSFPSVTMMTSVPAVVAKVPQIAIFTPP-APDGKVDAATLVAA 180 Query: 532 EKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDM 591 G + GGAQAVAA AYGT+T+ KI+GPG+ +V AAK + + + Sbjct: 181 RLAGVETVYKVGGAQAVAAAAYGTDTVTPALKIVGPGSPWVVAAKRLL----AGVIDPGL 236 Query: 592 PAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAV--HNQ 649 PAGPSE +++ADE A DLL +AEHG DS L V S + +E A+ H Sbjct: 237 PAGPSESIILADETVHGGLAALDLLIEAEHGPDSSAWL--VTHSRQVAEEALAALPSHWA 294 Query: 650 ALQLPRVDIVRK--CIAHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAG 707 A+ RVD + C IVL EE+ N YAPEHL + +++ + A Sbjct: 295 AMTPQRVDFSQAVLCGRAGGIVLTGSAEESHAFVNDYAPEHLQILSEKPFEHLGRITEAA 354 Query: 708 SVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRA 767 V +G +TP + ++ G N LPT AR + + F + + +T + Sbjct: 355 EVLMGPHTPITIANFCLGPNAVLPTSRGARTWGPLSVHDFLRRSSVGYVTAPAYPELAEV 414 Query: 768 VMCVAKKEGLDGHRNAV 784 +A+ EG H NAV Sbjct: 415 AKRLAEYEGFSSHGNAV 431 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: 699 Number of extensions: 25 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: 441 Length adjustment: 37 Effective length of query: 762 Effective length of database: 404 Effective search space: 307848 Effective search space used: 307848 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 16 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