Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_011023136.1 MA_RS16720 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000007345.1:WP_011023136.1 Length = 433 Score = 341 bits (875), Expect = 4e-98 Identities = 178/406 (43%), Positives = 263/406 (64%), Gaps = 7/406 (1%) Query: 382 SEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMKEALD 441 +++ V+ ++ +VR +G++AL EYT+KFD V+L+ ++ EE G+ E+ E L Sbjct: 28 ADVGETVSSVLSDVRVRGDAALREYTKKFDKVELAGFEVSEAEFEEALSGVGPELLEHLK 87 Query: 442 LSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVP 501 ++ N+R FH AQLP T +E QPGV+ + +E VG Y PGG A PST LM +P Sbjct: 88 VAAANIRVFHEAQLPETTWFMEVQPGVVLGQKATALESVGAYAPGGRASYPSTVLMTVIP 147 Query: 502 AQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKV 561 A+VA K+++ +PPR +DG + P + A+ GA K+ GG QAV AMAYGTET+PKV Sbjct: 148 ARVAGVKQVIVCTPPR-ADGSIHPLTLAAAKVAGADKVFKLGGVQAVGAMAYGTETVPKV 206 Query: 562 DKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEH 621 DKI+GPGN FVT+AKM V+N + ID PAGPSEVL+IAD+ AD VASD+++QAEH Sbjct: 207 DKIVGPGNVFVTSAKMQVRN----VAEIDFPAGPSEVLIIADDSADAAMVASDIIAQAEH 262 Query: 622 GIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVLCDGYEEALEMS 681 D + V V SE + ++ V QA R +IV+ + ++ +++ D E++++ S Sbjct: 263 --DPNAVSVLVTTSEILAEAVRQEVLLQAENTARSEIVKTSLENAAVLISDTLEQSIDFS 320 Query: 682 NQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSG 741 N++APEHL + + +++ + + NAGS+FVG Y P GDY+SGTNH LPT GYAR YSG Sbjct: 321 NKFAPEHLEIMVEDSDFVLNRIKNAGSIFVGNYAPVPVGDYASGTNHVLPTAGYARIYSG 380 Query: 742 ANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIR 787 N F K+ + Q I+ GLE++ ++ +A++EGL H +A++ R Sbjct: 381 LNINHFLKYSSIQKISKSGLESLKETIIALAEEEGLQAHADAIRTR 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: 686 Number of extensions: 35 Number of successful extensions: 4 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: 433 Length adjustment: 37 Effective length of query: 762 Effective length of database: 396 Effective search space: 301752 Effective search space used: 301752 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