Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_018123249.1 B149_RS0100770 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000375485.1:WP_018123249.1 Length = 436 Score = 236 bits (603), Expect = 1e-66 Identities = 154/432 (35%), Positives = 243/432 (56%), Gaps = 24/432 (5%) Query: 370 VQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYF 429 +Q+ L R +++ +V I++ +R +G++AL+EYT KFD K++ L P EE Sbjct: 17 IQQWLDRRKDPDTKVDGIVREILDTIRSRGDTALVEYTAKFDCPKITREQLTVP--EEII 74 Query: 430 EGLTE----EMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIP 485 G + E K+ L +I+NVR FH Q + G + + RP+++VGLY+P Sbjct: 75 LGALDSIPAEDKDILAEAIDNVRIFHEKQRENSWWTT-AEDGTILGQMVRPVDRVGLYVP 133 Query: 486 GGTA---ILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLA 542 GG L S+ +M +PAQVA + I SPPR+ DG ++P ++ A +G +I L+ Sbjct: 134 GGKGGETPLISSLIMNAIPAQVAGVESIAVTSPPRE-DGTLNPYILATAALLGLKEIHLS 192 Query: 543 GGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIA 602 G A A+ A+AYGTE+I D I GPGN FV AK + IDM AGPSE+ ++A Sbjct: 193 GSAWAIGALAYGTESIAPCDVIAGPGNIFVATAKSQLIGQI----GIDMVAGPSEIAILA 248 Query: 603 DEDADVDFVASDLLSQAEHGIDSQVILV--GVNLSEKKIQEIQDAVHNQALQLPRVDIVR 660 D+ A+ +++A+D+LSQAEH + ILV L+EK ++++ Q +LPR +I Sbjct: 249 DDSANPEWLAADMLSQAEHDPLAASILVTDSPELAEKTCEQLK----LQTAELPRGEIAA 304 Query: 661 KCIAH--STIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPES 718 K +A +TI++ D A ++ N+ APEHL L +A+ ++ + +AG++F+G ++PE Sbjct: 305 KALADWGATIIVEDLVTGA-DLINRIAPEHLELSLADPWSHLGAIRHAGAIFMGHHSPEP 363 Query: 719 CGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLD 778 GDY +G NH LPT R S + F K + +P + G + +A+ EGL+ Sbjct: 364 VGDYFAGPNHVLPTLRTVRFSSALSVQNFCKKSSVIAASPSYVAEHGDKIARLARLEGLE 423 Query: 779 GHRNAVKIRMSK 790 H +V+ R K Sbjct: 424 AHARSVECRNKK 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: 768 Number of extensions: 44 Number of successful extensions: 7 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 10 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