Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate YP_001327383.1 Smed_1713 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000017145.1:YP_001327383.1 Length = 432 Score = 221 bits (563), Expect = 6e-62 Identities = 147/415 (35%), Positives = 215/415 (51%), Gaps = 15/415 (3%) Query: 378 IQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEEMK 437 + T+ + V II NVR++G++A+ EY+ FD V+L ++ + L + + Sbjct: 23 VSDTAPVEKTVKEIIANVRERGDAAVREYSAAFDKVELEKFEVSQEERLKAVAELDPQTR 82 Query: 438 EALDLSIENVRKFHAAQLPTET-LEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTAL 496 E + +I NVR F AQL T LE+ET PG+ PIE VG Y+PGG L S + Sbjct: 83 EDTEFAIANVRAFAEAQLKTILPLEIETLPGLHLGHRVIPIEIVGCYVPGGRYPLLSAPV 142 Query: 497 MLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTE 556 M VPA+VA C +++ PP P ++ GA +I GGAQA+AAMA GTE Sbjct: 143 MTIVPAKVAGCDQVIACLPPN-----AHPAMIAGCHLSGADRIFRVGGAQAIAAMASGTE 197 Query: 557 TIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLL 616 TIP VDKI+GPGN FV AK V ID AGPSE+ ++ADE +A+DLL Sbjct: 198 TIPAVDKIVGPGNAFVNEAKRQVFGQV----GIDQLAGPSEIFIVADETGKAAMIATDLL 253 Query: 617 SQAEHGIDSQVILVGVN--LSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVLCDGY 674 +QAEH + ++V L+ + L+E+ + E++ + Q L V V + I +C+ Sbjct: 254 AQAEHDVRTRVGLITTDRKLAEETLVEVEKQL--QDLSTANVASV-AWKDYGEITVCEDE 310 Query: 675 EEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYG 734 + S+ A EHL + + + + N GS+F+G D GTNHTLPT Sbjct: 311 TTMIAYSDYIAAEHLQVHTRDPQATARKLRNYGSLFIGELASVVYSDKCCGTNHTLPTMA 370 Query: 735 YARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789 R G ++ K T Q + G+ + A + + E L+GHR A +R+S Sbjct: 371 AGRYTGGLWVGSYLKTCTHQWLDERGVAAVAPAAVRQSATERLEGHRRAAALRLS 425 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: 629 Number of extensions: 34 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: 432 Length adjustment: 37 Effective length of query: 762 Effective length of database: 395 Effective search space: 300990 Effective search space used: 300990 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