Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate SMc02307 SMc02307 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >FitnessBrowser__Smeli:SMc02307 Length = 434 Score = 264 bits (674), Expect = 9e-75 Identities = 162/436 (37%), Positives = 244/436 (55%), Gaps = 12/436 (2%) Query: 357 IHLDVVKASDKVGVQKALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVK-- 414 I L+ + S + L+ + + ++ +V II++VR +G++AL +Y+ +FDG+ Sbjct: 3 IRLNYLDTSFERDFAAFLTTKREVSEDVNAVVRAIIDDVRARGDAALADYSARFDGIDFT 62 Query: 415 LSNPVLNAPFPEEYFEGLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFP 474 ++ + + + + E+ AL ++ + H QLP + + E Q GV Sbjct: 63 VTGMAVTSAEIDAAIHAVAPEVLGALKVAATRIEAHHRRQLPKDDI-YEDQMGVGLGSRW 121 Query: 475 RPIEKVGLYIPGGTAILPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKV 534 PI+ VGLY+PGGTA PS+ LM +PA+VA IV P S G ++P V+ A Sbjct: 122 TPIDAVGLYVPGGTASYPSSVLMNALPAKVAGVPRIVMVVPA--SGGSINPAVLAAARLA 179 Query: 535 GASKIVLAGGAQAVAAMAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAG 594 G +I GGAQAVAA+AYGTETI V KI+GPGN +V AAK V IDM AG Sbjct: 180 GVEEIYRIGGAQAVAALAYGTETIEPVAKIVGPGNAYVAAAKRQVFGTV----GIDMIAG 235 Query: 595 PSEVLVIADEDADVDFVASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLP 654 PSEVLVIAD D D D++A+DLL+QAEH +Q IL+ + + ++ AV Q LP Sbjct: 236 PSEVLVIADRDNDPDWIAADLLAQAEHDAGAQAILITDDAAFG--DAVEKAVERQLKTLP 293 Query: 655 RVDIVRKCIAH-STIVLCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGA 713 R + ++L +++A+ ++N+ APEHL L A+ + V + NAG++F+G Sbjct: 294 RAETAAASWRDFGAVILVPDFDKAVPLANRIAPEHLELATADPDAMVPAIRNAGAIFIGR 353 Query: 714 YTPESCGDYSSGTNHTLPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAK 773 +TPE GDY G+NH LPT AR SG + K + + P+ L +G A + +A+ Sbjct: 354 HTPEVIGDYVGGSNHVLPTARSARFSSGLGVLDYVKRTSILRLGPDQLRILGPAAIALAR 413 Query: 774 KEGLDGHRNAVKIRMS 789 EGL+ H +V IR++ Sbjct: 414 SEGLEAHARSVAIRLN 429 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: 613 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: 434 Length adjustment: 37 Effective length of query: 762 Effective length of database: 397 Effective search space: 302514 Effective search space used: 302514 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