Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate BPHYT_RS17710 BPHYT_RS17710 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__BFirm:BPHYT_RS17710 Length = 440 Score = 239 bits (609), Expect = 3e-67 Identities = 153/441 (34%), Positives = 232/441 (52%), Gaps = 15/441 (3%) Query: 359 LDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSN- 417 LD + + L+ + I V I+ +V+ +G++A+LEYT++FD V+ + Sbjct: 8 LDSTAPDFQKSLHAVLAFEASEDEAIERSVAQILNDVKARGDAAVLEYTQRFDRVEAKSV 67 Query: 418 PVLNAPFPE--EYFEGLTEEMKEALDLSIENVRKFHAAQ---LPTETLEVETQPGVLCSR 472 L P E E L + + AL+ + VR +H Q + + + G + + Sbjct: 68 DALELPMSELEAALENLEPKRRAALEAAAARVRGYHEKQKIECGSHSWQYTEADGTVLGQ 127 Query: 473 FPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAE 532 P+++ G+Y+PGG A PS+ LM +PA+VA +EIV P DG +P V+ A Sbjct: 128 KVTPLDRAGIYVPGGKAAYPSSVLMNAIPARVAGVREIVMVVPT--PDGVKNPLVLAAAL 185 Query: 533 KVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMP 592 G ++ GGAQAV A+AYGT TIP VDKI GPGN +V +AK V IDM Sbjct: 186 LGGVDRVFTIGGAQAVGALAYGTATIPAVDKICGPGNAYVASAKRRVFGTV----GIDMI 241 Query: 593 AGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQ 652 AGPSE+LV+ D D +VA DL SQAEH +Q IL+ + + I ++DA+ Sbjct: 242 AGPSEILVLCDGTTDPRWVAMDLFSQAEHDELAQSILLCPD--DAFIGRVKDAIDELLPT 299 Query: 653 LPRVDIVRKCIA-HSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFV 711 +PR D++RK + ++ E+A ++N APEHL + + + +L+ +AG++F+ Sbjct: 300 MPRRDVIRKSLEDRGALIKVRDMEQACAIANDIAPEHLEISALEPHHWGQLIRHAGAIFL 359 Query: 712 GAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCV 771 G YT ES GDY +G NH LPT AR S F K + ++ EG + +G + Sbjct: 360 GRYTSESLGDYCAGPNHVLPTSRTARFSSPLGVYDFFKRSSVIEVSAEGAQTLGEIAAEL 419 Query: 772 AKKEGLDGHRNAVKIRMSKLG 792 A EGL H + + RM + G Sbjct: 420 AYGEGLQAHARSAEYRMRQNG 440 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: 713 Number of extensions: 33 Number of successful extensions: 6 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: 440 Length adjustment: 37 Effective length of query: 762 Effective length of database: 403 Effective search space: 307086 Effective search space used: 307086 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