Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate H281DRAFT_05652 H281DRAFT_05652 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Burk376:H281DRAFT_05652 Length = 440 Score = 236 bits (602), Expect = 2e-66 Identities = 151/442 (34%), Positives = 230/442 (52%), Gaps = 17/442 (3%) Query: 359 LDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNP 418 LD + + L+ + I V I+ +V+ +G++A+LEYT +FD + +N Sbjct: 8 LDSTARDFQKSLHAVLAFEASEDEAIERSVAQILSDVKARGDAAVLEYTNRFDRLS-ANS 66 Query: 419 VLNAPFP----EEYFEGLTEEMKEALDLSIENVRKFHAAQ---LPTETLEVETQPGVLCS 471 V P E EGL + + AL+ + VR +H Q + + + G + Sbjct: 67 VAALELPMSELEAALEGLEPKRRAALEAAAARVRGYHEKQKIECGSHSWQYTEADGTVLG 126 Query: 472 RFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVA 531 + P+++ G+Y+PGG A PS+ LM +PA+VA +EIV P DG +P V+ A Sbjct: 127 QKVTPLDRAGIYVPGGKAAYPSSVLMNAIPARVAGVREIVMVVPT--PDGVKNPLVLAAA 184 Query: 532 EKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDM 591 G ++ GGAQAV A+AYGT+T+P VDKI GPGN +V +AK V IDM Sbjct: 185 LLGGVDRVFTIGGAQAVGALAYGTQTVPAVDKICGPGNAYVASAKRRVFGTV----GIDM 240 Query: 592 PAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQAL 651 AGPSE+LV+ D D +VA DL SQAEH +Q IL+ + + I + DA++ Sbjct: 241 IAGPSEILVLCDGTTDPRWVAMDLFSQAEHDELAQSILLCPD--DAFIGRVNDAINELLP 298 Query: 652 QLPRVDIVRKCI-AHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVF 710 +PR D+++ + ++ EA ++N APEHL + + + +L+ +AG++F Sbjct: 299 TMPRRDVIQASLEGRGALIKVRDMAEACAIANDIAPEHLEISALEPHQWGQLIRHAGAIF 358 Query: 711 VGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMC 770 +G YT ES GDY +G NH LPT AR S F K + ++ EG + +G Sbjct: 359 LGRYTSESLGDYCAGPNHVLPTSRTARFSSPLGVYDFFKRSSVIEVSAEGAQTLGEIAAE 418 Query: 771 VAKKEGLDGHRNAVKIRMSKLG 792 +A EGL H + + RM G Sbjct: 419 LAYGEGLQAHARSAEYRMRHSG 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: 679 Number of extensions: 31 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: 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