Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_011385702.1 AMB_RS16905 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000009985.1:WP_011385702.1 Length = 433 Score = 257 bits (657), Expect = 8e-73 Identities = 162/420 (38%), Positives = 231/420 (55%), Gaps = 14/420 (3%) Query: 373 ALSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLN--APFPEEYFE 430 A+ R + + ++ V I+ VR +G++AL+EYT +FD ++L+ L A E + Sbjct: 21 AMKREVDE--DVDQAVAAILAEVRSRGDAALIEYTARFDRLELTPATLRITAQEVETAYA 78 Query: 431 GLTEEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAI 490 E+ AL+L+ E +R FHA Q+P + + GV P+ GLY+PGGTA Sbjct: 79 SCDPELIRALELAAERIRAFHARQVPVDDSFTDAA-GVRLGLRWSPVSAAGLYVPGGTAA 137 Query: 491 LPSTALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAA 550 PS+ LM +PA+ A + +V P G ++P V+ A+ G +I GGAQAV A Sbjct: 138 YPSSVLMNAIPAKAAGVERLVMVVP--SPGGVLNPLVLAAAKVAGVDEIYRVGGAQAVGA 195 Query: 551 MAYGTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDF 610 +AYGT TI VDKI+GPGN +V AAK V IDM AGPSE+LV+AD D + Sbjct: 196 LAYGTGTIRPVDKIVGPGNAWVAAAKRRVFGTV----GIDMIAGPSEILVVADRFNDPSW 251 Query: 611 VASDLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCI-AHSTIV 669 +A+DLLSQAEH +Q IL+ + Q + AV + LPR I R+ +H I+ Sbjct: 252 IAADLLSQAEHDTAAQSILITDDAEFG--QRVAAAVESHLATLPRAKIARESWDSHGAII 309 Query: 670 LCDGYEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHT 729 + E +L + ++ APEHL L + N + V NAG++F+G YTPE+ GDY G NH Sbjct: 310 VVPDLEASLPLIDRIAPEHLELAVENPDALAARVRNAGAIFLGRYTPEAVGDYIGGPNHV 369 Query: 730 LPTYGYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMS 789 LPT AR SG F K T + L IG A + +A+ EGL H +V +R++ Sbjct: 370 LPTARSARFSSGLGVLDFMKRTTLLGCDADSLRAIGPAAVRLAEAEGLGAHGLSVALRLN 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: 658 Number of extensions: 29 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: 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