Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_013554303.1 NITSA_RS06905 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000186245.1:WP_013554303.1 Length = 431 Score = 256 bits (655), Expect = 1e-72 Identities = 155/426 (36%), Positives = 238/426 (55%), Gaps = 17/426 (3%) Query: 371 QKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEY-- 428 ++ L R ++ V +++ +R++GN+AL + +FD + ++ P E Sbjct: 16 EELLGRGAMDIDQVTETVAALLKEIREEGNAALRRHIARFDRWEPADDAALQVDPAEMAM 75 Query: 429 -FEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGG 487 +E + E+++AL L+ + ++ +H LP E E +L + P+++ GLYIPGG Sbjct: 76 AYEAIAPELRDALHLAYDRIKAYHEKLLPKSWFEYEKNGSMLGQKVT-PVDRAGLYIPGG 134 Query: 488 TAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQA 547 A PS+ LM VPA VA +EIV +P D +++ ++ G K+ GGA A Sbjct: 135 KAAYPSSLLMNAVPAIVAGVEEIVVCTPT--PDNEINVLLLAACHLCGIKKVFKVGGASA 192 Query: 548 VAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDAD 607 + AMAYGTETIPKVD I GPGN FV AK V + +IDM AGPSE+ ++AD A Sbjct: 193 IGAMAYGTETIPKVDVITGPGNIFVATAKKLVYGEV----NIDMIAGPSEIGILADGSAR 248 Query: 608 VDFVASDLLSQAEHGIDSQVILV--GVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH 665 D+VA DLLSQAEH + IL+ L+++ + E++ A+ +L R I RK I Sbjct: 249 PDWVAMDLLSQAEHDEMASSILITDDAELAKRVVDEVEKALS----KLEREAIARKSIEE 304 Query: 666 -STIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSS 724 I++ EA+++ NQ APEHL + A+ + + + +AG++F+G YTPE GDY + Sbjct: 305 RGAIIVTSDMAEAIDLMNQIAPEHLEVMTASPMELLGSIKHAGAIFLGHYTPEPIGDYIA 364 Query: 725 GTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAV 784 G NHTLPT G A+ YS + F K + +T G+ +G A +A EGL H +V Sbjct: 365 GPNHTLPTGGTAKFYSPLSVEHFLKKSSLIMMTEAGVRELGDACALLAHTEGLTAHEASV 424 Query: 785 KIRMSK 790 +IR+ + Sbjct: 425 RIRLEE 430 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: 735 Number of extensions: 42 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: 431 Length adjustment: 37 Effective length of query: 762 Effective length of database: 394 Effective search space: 300228 Effective search space used: 300228 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