Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_012284033.1 HM1_RS13880 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000019165.1:WP_012284033.1 Length = 426 Score = 269 bits (687), Expect = 3e-76 Identities = 162/406 (39%), Positives = 235/406 (57%), Gaps = 12/406 (2%) Query: 388 VNPIIENVRDKGNSALLEYTEKFDGVKL--SNPVLNAPFPEEYFEGLTEEMKEALDLSIE 445 V +I NVR++G +AL YT++FDG + SN ++ + + + + AL + E Sbjct: 30 VAEVIANVRNQGTAALFAYTKRFDGADVDESNFRVSEAEIDAAYSQVDPSVLAALRRACE 89 Query: 446 NVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVA 505 N+R+FH QL +E E G + + RP+E+VG+Y+PGG A PS+ LM VPA+VA Sbjct: 90 NIRRFHEKQLRPSWIEPEAD-GTMLGQLIRPLERVGVYVPGGLASYPSSVLMNAVPAKVA 148 Query: 506 QCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKIL 565 ++V A+PP K DG ++P + A++ G ++ GGAQAVAAMA+G + VDKI Sbjct: 149 GVPQVVMATPPGK-DGSINPYSLVAAKEAGVDEVYRMGGAQAVAAMAFGVG-LKAVDKIT 206 Query: 566 GPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDS 625 GPGN +VT AK V IDM AGPSEVLVIADE A +VA+D LSQAEH + + Sbjct: 207 GPGNIYVTLAKKQVYGTVD----IDMLAGPSEVLVIADESAAPAYVAADFLSQAEHDVRA 262 Query: 626 QVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIA-HSTIVLCDGYEEALEMSNQY 684 +LV S ++ + Q LPR +I+ + + + I + EEA ++SN++ Sbjct: 263 ATVLV--TPSAALADAVEAEIARQLATLPRREIMEQALRDNGAIFIVKDLEEACQVSNRF 320 Query: 685 APEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANT 744 APEHL + + + AG++F+G Y+PE GDY +G NH LPT G AR YS N Sbjct: 321 APEHLEVLTEAPFALLGKLTQAGAIFLGPYSPEPVGDYFAGPNHVLPTGGTARFYSPLNV 380 Query: 745 ATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSK 790 TFQK + + + + ++ +AK EGLD H NAV +R+ K Sbjct: 381 DTFQKKTSLIAYSKVRFDRDAKDIIALAKAEGLDAHANAVAVRLEK 426 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: 692 Number of extensions: 38 Number of successful extensions: 8 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: 426 Length adjustment: 36 Effective length of query: 763 Effective length of database: 390 Effective search space: 297570 Effective search space used: 297570 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