Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_012566836.1 RC1_RS07905 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000016185.1:WP_012566836.1 Length = 433 Score = 236 bits (602), Expect = 2e-66 Identities = 161/438 (36%), Positives = 223/438 (50%), Gaps = 12/438 (2%) Query: 356 PIHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKL 415 P+ L + G L+ + ++ V ++ +VR G++A++ YT ++D L Sbjct: 2 PLRLSTRDPGFEAGFATLLAAKREVQEDVNAAVATVLADVRAHGDTAVIGYTRRWDRQDL 61 Query: 416 SNPVLNAPFPE--EYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRF 473 + L E AL + + FH Q P E L GV Sbjct: 62 TPETLRITAAEIDAAVARCDAGTLAALHEAAARIEAFHRRQQP-EALSFTDAQGVRLGAR 120 Query: 474 PRPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEK 533 P+ VG+Y+PGGTA PS+ LM +PA+VA I P DG ++P V+ A Sbjct: 121 WTPVGAVGIYVPGGTAAYPSSVLMNAMPARVAGVPRIAMVVPT--PDGVLNPLVLAAARA 178 Query: 534 VGASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPA 593 G ++I GGAQAVAA+AYGT+TI VDKI+GPGN +V AAK V IDM A Sbjct: 179 AGVTEIYRIGGAQAVAALAYGTDTIAPVDKIVGPGNAYVAAAKRQVFGTV----GIDMIA 234 Query: 594 GPSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQL 653 GPSE+LV+AD D ++A+DLLSQAEH SQ IL+ + + + AV L Sbjct: 235 GPSEILVVADGANDPAWIAADLLSQAEHDESSQAILLTDDAAFA--DAVAAAVEAHLATL 292 Query: 654 PRVDIVRKCI-AHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVG 712 PR I AH IV+ EA + ++ APEHL L +A+ + V NAG++F+G Sbjct: 293 PRARIAAASWQAHGAIVVLRDLAEAPALVDRLAPEHLELAVADPDALAARVRNAGAIFLG 352 Query: 713 AYTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVA 772 +TPE+ GDY +G NH LPT AR SG N F K T L IG A + +A Sbjct: 353 RHTPEAIGDYVAGPNHVLPTARSARFSSGLNVLDFMKRTTLVGCDACSLAAIGPAAVTLA 412 Query: 773 KKEGLDGHRNAVKIRMSK 790 + EGL+ H +V IR+ + Sbjct: 413 RAEGLEAHALSVAIRLGR 430 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: 639 Number of extensions: 26 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