Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_066326079.1 BLR17_RS14020 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_900100165.1:WP_066326079.1 Length = 427 Score = 382 bits (981), Expect = e-110 Identities = 208/418 (49%), Positives = 273/418 (65%), Gaps = 7/418 (1%) Query: 374 LSRPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLT 433 L RP + ++I V I V+ G++A+ +YT +FDGV N + A E ++ Sbjct: 16 LERPTKTVNDIEATVKEIFAAVQKDGDAAVAKYTTQFDGVYFENSEVTAAEIEVAINTIS 75 Query: 434 EEMKEALDLSIENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPS 493 +E+ A+ L+ NV KFH AQ T + +ET GV C + RPI+KVGLYIPGGTA L S Sbjct: 76 DELTAAISLAKANVEKFHQAQKTTR-VSIETAEGVQCWQEKRPIQKVGLYIPGGTAPLFS 134 Query: 494 TALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAY 553 T LML VPA++A C EIV SPP K+ G ++P ++Y A G +KI+ GG QA+A M + Sbjct: 135 TVLMLAVPAKIAGCSEIVLCSPPDKN-GNINPAILYAANLCGVTKIIKVGGIQAIAGMTF 193 Query: 554 GTETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVAS 613 GT+ IPKV KI GPGNQ+VT AK Q TQ +IDMPAGPSE+LV+AD+ A FVAS Sbjct: 194 GTKAIPKVYKIFGPGNQYVTVAK---QLATQFGVAIDMPAGPSELLVVADDTAVPAFVAS 250 Query: 614 DLLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVLCDG 673 DLLSQAEHG+DSQVILV S+ I ++ + Q LPR I K IA+S + + Sbjct: 251 DLLSQAEHGVDSQVILVST--SKAMIDAVESEIQAQLELLPRKTIAEKAIANSKSIFVEN 308 Query: 674 YEEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTY 733 AL++ N+Y PEH I+ AN + YV + NAGSVF+G YTPES GDY+SGTNHTLPT Sbjct: 309 DSIALDLINEYGPEHFIVCTANNDFYVDGIQNAGSVFIGNYTPESAGDYASGTNHTLPTN 368 Query: 734 GYARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKL 791 GYA+ YSG N +F K +T Q I+ +G++NIG A+ +A+ EGL HRNAV +R+ L Sbjct: 369 GYAKNYSGVNLDSFMKSMTFQKISEKGIQNIGTAIEVMAEAEGLQAHRNAVTLRLKSL 426 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: 757 Number of extensions: 30 Number of successful extensions: 5 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: 427 Length adjustment: 36 Effective length of query: 763 Effective length of database: 391 Effective search space: 298333 Effective search space used: 298333 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 Jul 26 2024. The underlying query database was built on Jul 25 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