Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_010527284.1 GQW_RS0106975 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000220155.1:WP_010527284.1 Length = 426 Score = 386 bits (991), Expect = e-111 Identities = 210/417 (50%), Positives = 280/417 (67%), Gaps = 9/417 (2%) Query: 376 RPIQKTSEIMHLVNPIIENVRDKGNSALLEYTEKFDGVKLSNPVLNAPFPEEYFEGLTEE 435 R I E+M V PI++ V+ + AL E T +FDG++LSN + ++ + + Sbjct: 18 RAIVDQQEVMEKVKPILQAVKQHKDKALQELTAQFDGIELSNFEVTEEEIKQGCLDVDSQ 77 Query: 436 MKEALDLSIENVRKFHAAQ-LPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPST 494 +K A++ + N+R FH +Q LP + ++ET PGV C + PIEKVGLYIPGG+A L ST Sbjct: 78 LKGAINSARINIRHFHESQQLPIK--KIETTPGVQCWQRSTPIEKVGLYIPGGSAPLFST 135 Query: 495 ALMLGVPAQVAQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYG 554 LML +PA +A CKEIV SPP K +GK+ P +++ A G +KI GGAQA+AAMAYG Sbjct: 136 VLMLAIPATIAGCKEIVLCSPPDK-EGKIHPAILFAAHLTGVTKIFKVGGAQAIAAMAYG 194 Query: 555 TETIPKVDKILGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASD 614 TETIPKVDKI GPGN FVTAAK V D A ID+PAGPSEV V+ADE A +FVASD Sbjct: 195 TETIPKVDKIFGPGNSFVTAAKQLVTLDGIA---IDLPAGPSEVAVMADESAHPEFVASD 251 Query: 615 LLSQAEHGIDSQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAHSTIVLCDGY 674 LLSQAEHG DSQ IL+ SE+ ++ A++ Q LPR+ +K + +S I+L Sbjct: 252 LLSQAEHGPDSQSILI--TDSEQLANDVTIAINEQLKSLPRIYTAKKALENSRIILLSNL 309 Query: 675 EEALEMSNQYAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYG 734 +E ++ SN YAPEHLIL + N N + + NAGSVF+G +TPES GDY+SGTNHTLPTYG Sbjct: 310 DEMIDFSNLYAPEHLILAVRNPNYVAEKITNAGSVFLGHFTPESAGDYASGTNHTLPTYG 369 Query: 735 YARQYSGANTATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRMSKL 791 YAR YSG N +F K IT Q IT +GL+ +G + +A+ E L+ H+ A+ +R++K+ Sbjct: 370 YARAYSGVNLDSFCKKITFQEITKDGLKKLGPIIETMAEAEQLEAHKMAISVRLNKI 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: 738 Number of extensions: 33 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: 426 Length adjustment: 36 Effective length of query: 763 Effective length of database: 390 Effective search space: 297570 Effective search space used: 297570 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