Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate PP_0966 PP_0966 Histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Putida:PP_0966 Length = 441 Score = 248 bits (632), Expect = 7e-70 Identities = 143/402 (35%), Positives = 230/402 (57%), Gaps = 13/402 (3%) Query: 391 IIENVRDKGNSALLEYTEKFDGV---KLSNPVLNAPFPEEYFEGLTEEMKEALDLSIENV 447 II+ VR++G++AL+E+T++FDGV + + +L+ E +T +EAL+ + V Sbjct: 42 IIKAVRERGDAALVEFTQRFDGVDAKSIDDLILDRARLELALTRITPVQREALEKAANRV 101 Query: 448 RKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQC 507 R +H Q ++ + G + + P+++ GLY+PGG A PS+ LM +PA+VA Sbjct: 102 RIYHERQ-KQDSWQYTEADGTVLGQKVTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGV 160 Query: 508 KEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGP 567 E+V P + G+V+ V+ A G ++ GGAQAVAA+AYGTE++P+VDKI+GP Sbjct: 161 TEVVMVVPTPR--GEVNELVLAAACIAGVDRVFTVGGAQAVAALAYGTESVPQVDKIVGP 218 Query: 568 GNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQV 627 GN +V AK +V IDM AGPSE+LV+ D D D++A DL SQAEH D+Q Sbjct: 219 GNIYVATAKRHVFGQV----GIDMIAGPSEILVVCDGQTDPDWIAMDLFSQAEHDEDAQA 274 Query: 628 ILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI-AHSTIVLCDGYEEALEMSNQYAP 686 ILV + + + + ++ + R DI+ K I ++ ++A++++N+ AP Sbjct: 275 ILVSPDAAF--LDRVAASIDKLMPTMERADIIEKSINGRGALIQVRDMQQAMDVANRIAP 332 Query: 687 EHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTAT 746 EHL L +A+ ++ + +AG++F+G +T E+ GDY +G NH LPT G AR S Sbjct: 333 EHLELSVADPQAWLPHIRHAGAIFMGRHTSEALGDYCAGPNHVLPTSGTARFSSPLGVYD 392 Query: 747 FQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 FQK + + +G +G +A+ E L H + + R+ Sbjct: 393 FQKRSSIIFCSEQGASELGHTASVLARGESLTAHARSAEYRI 434 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: 694 Number of extensions: 40 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: 441 Length adjustment: 37 Effective length of query: 762 Effective length of database: 404 Effective search space: 307848 Effective search space used: 307848 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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