Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate YP_001325902.1 Smed_0208 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000017145.1:YP_001325902.1 Length = 434 Score = 266 bits (679), Expect = 2e-75 Identities = 160/412 (38%), Positives = 234/412 (56%), Gaps = 12/412 (2%) Query: 381 TSEIMHLVNPIIENVRDKGNSALLEYTEKFDGV--KLSNPVLNAPFPEEYFEGLTEEMKE 438 + ++ +V II++VR +G++AL +Y+ +FDG+ ++ + A + + E+ Sbjct: 27 SEDVNAVVRDIIDDVRARGDAALADYSARFDGIDFNVTGMAVTAAEIDAAIHAVAPEVLG 86 Query: 439 ALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALML 498 AL ++ + H QLP + + E Q GV PI+ VGLY+PGGTA PS+ LM Sbjct: 87 ALKVAATRIEAHHRRQLPKDDI-YEDQMGVGLGSRWTPIDAVGLYVPGGTASYPSSVLMN 145 Query: 499 GVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETI 558 +PA+VA IV P G V+P V+ A G +I GGAQAVAA+AYGT TI Sbjct: 146 ALPAKVAGVPRIVMVVPAM--GGAVNPAVLAAARLAGVEEIYRIGGAQAVAALAYGTGTI 203 Query: 559 PKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQ 618 V KI+GPGN +V AAK V IDM AGPSEVLVIAD D D D++A+D+L+Q Sbjct: 204 APVAKIMGPGNAYVAAAKRQVFGTV----GIDMIAGPSEVLVIADRDNDPDWIAADMLAQ 259 Query: 619 AEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYEEA 677 AEH +Q IL+ + + +++AV Q LPR D I+L +++A Sbjct: 260 AEHDAGAQAILITDDAAFG--DAVEEAVERQLKTLPRADTAAASWRDFGAIILVPDFDKA 317 Query: 678 LEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYAR 737 + ++N+ APEHL L A+ + V + NAG++F+G +TPE GDY G+NH LPT AR Sbjct: 318 IPLANRIAPEHLELATADPDAMVPAIRNAGAIFIGRHTPEVIGDYVGGSNHVLPTARSAR 377 Query: 738 QYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789 SG + K + + PE L +G A + +A+ EGL+ H +V IR++ Sbjct: 378 FSSGLGVLDYMKRTSILRLDPEQLRILGPAAIALARSEGLEAHARSVAIRLN 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: 615 Number of extensions: 22 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 10 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