Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate GFF3235 Psest_3298 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__psRCH2:GFF3235 Length = 436 Score = 260 bits (664), Expect = 1e-73 Identities = 150/402 (37%), Positives = 232/402 (57%), Gaps = 13/402 (3%) Query: 391 IIENVRDKGNSALLEYTEKFDGVKLSNP---VLNAPFPEEYFEGLTEEMKEALDLSIENV 447 II+ VR++G++AL+E T++FDG+++++ +L E+ E +T +EAL+++ E V Sbjct: 42 IIKAVRERGDAALVELTQRFDGLQVASMADLILPRARLEQALERITPAQREALEIAAERV 101 Query: 448 RKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQC 507 +H Q E VL + P+++ GLY+PGG A PS+ LM +PA+VA Sbjct: 102 SSYHERQKQDSWTYTEADGTVLGQKVT-PLDRAGLYVPGGKASYPSSVLMNAIPAKVAGV 160 Query: 508 KEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKILGP 567 E+V P + G+++ V+ A G ++ GGAQAVAA+AYGTE++P VDKI+GP Sbjct: 161 PEVVMVVPTPR--GELNELVLAAACIAGVDRVFTIGGAQAVAALAYGTESVPPVDKIVGP 218 Query: 568 GNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGIDSQV 627 GN +V AK +V IDM AGPSE+LV+ D D D++A DL SQAEH D+Q Sbjct: 219 GNIYVATAKRHVFGKV----GIDMIAGPSEILVVCDGQTDPDWIAMDLFSQAEHDEDAQS 274 Query: 628 ILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI-AHSTIVLCDGYEEALEMSNQYAP 686 ILV + + + + +++ L R DI R I ++L ++A+E++N+ AP Sbjct: 275 ILVSPDA--EFLDRVAESIARLLPTLERADIARTSIEGRGALILVADMQQAIEVANRIAP 332 Query: 687 EHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGANTAT 746 EHL L +A ++ + +AG++F+G YT E+ GDY +G NH LPT G AR S Sbjct: 333 EHLELSVAEPEQWLPQIRHAGAIFMGRYTAEALGDYCAGPNHVLPTSGTARFSSPLGVYD 392 Query: 747 FQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 FQK + N + EG +G+ +A+ E L H + + R+ Sbjct: 393 FQKRSSIINCSAEGASTLGKVASVLARGESLTAHARSAEYRI 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: 734 Number of extensions: 35 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: 436 Length adjustment: 37 Effective length of query: 762 Effective length of database: 399 Effective search space: 304038 Effective search space used: 304038 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