Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate 3608641 Dshi_2034 Histidinol dehydrogenase (RefSeq)
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Dino:3608641 Length = 435 Score = 240 bits (612), Expect = 1e-67 Identities = 146/427 (34%), Positives = 228/427 (53%), Gaps = 16/427 (3%) Query: 370 VQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDG----VKLSNPVLNAPFP 425 ++KA P E +V I++ + G+ A L Y KFD + LS ++A Sbjct: 6 LKKATLTPKSDAGETKKIVRAILDEIEAGGDDAALAYARKFDNYEGEILLSQDAIDAAIA 65 Query: 426 EEYFEGLTEEMKEALDLSIENVRKFHAAQLPT-ETLEVETQPGVLCSRFPRPIEKVGLYI 484 + + E++K +D + NV++F AQ T E+E PG++ + P+ G Y+ Sbjct: 66 Q-----VPEKLKHDIDFAHANVKRFAEAQRDTVANFEIEVVPGLIAGQKAIPVHAAGCYV 120 Query: 485 PGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGG 544 PGG ++A+M A+VA CK IV SPPR G ++P +VY A GA KI+ GG Sbjct: 121 PGGRYSHIASAIMTVTTAKVAGCKHIVACSPPRPDVG-IAPAIVYAAHVCGADKIMAMGG 179 Query: 545 AQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADE 604 Q VAAM +G +PK + ++GPGNQFV AK + IDM AGP++ L++AD Sbjct: 180 VQGVAAMTFGLFGLPKANILVGPGNQFVAEAKRMLFGRV----GIDMIAGPTDSLILADA 235 Query: 605 DADVDFVASDLLSQAEHGIDSQVILVGVNLS-EKKIQEIQDAVHNQALQLPRVDIVRKCI 663 AD VA DL+ QAEHG +S V LV + + +K+ E+ + + + R + Sbjct: 236 SADPMVVAVDLVGQAEHGYNSPVWLVTDDRALAEKVMELVPGLIDDLPDVNRENATAAWR 295 Query: 664 AHSTIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYS 723 ++ +++C EE S++YAPEHL +Q + + +++ + GS+F+G T + GD + Sbjct: 296 DYAEVIVCADREEMAATSDEYAPEHLTVQAEDLDWWLERLSCYGSLFLGEETTVAFGDKA 355 Query: 724 SGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNA 783 SGTNH LPT G A G + + K +T Q T EG + + A +++ EG++GH Sbjct: 356 SGTNHVLPTSGAANYTGGLSVHKYMKIVTWQRSTREGSKPVALATARISRLEGMEGHART 415 Query: 784 VKIRMSK 790 IR+ K Sbjct: 416 ADIRLRK 422 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: 722 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: 435 Length adjustment: 37 Effective length of query: 762 Effective length of database: 398 Effective search space: 303276 Effective search space used: 303276 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