Align Histidine biosynthesis trifunctional protein; EC 3.5.4.19; EC 3.6.1.31; EC 1.1.1.23 (characterized)
to candidate WP_029133632.1 A3GO_RS0112245 histidinol dehydrogenase
Query= SwissProt::P00815 (799 letters) >NCBI__GCF_000428045.1:WP_029133632.1 Length = 432 Score = 251 bits (642), Expect = 4e-71 Identities = 150/405 (37%), Positives = 220/405 (54%), Gaps = 13/405 (3%) Query: 388 VNPIIENVRDKGNSALLEYTEKFDGVKLSNPV-LNAPFP--EEYFEGLTEEMKEALDLSI 444 VN II N+R +G+ ALLEYT +FDG + L P E+ + + E + AL + Sbjct: 36 VNEIIANIRQRGDEALLEYTNRFDGWNAAGAADLEVPLARLEQAWNTIPEAQQTALKHAA 95 Query: 445 ENVRKFHAAQLPTETLEVETQPGVLCSRFPRPIEKVGLYIPGGTAILPSTALMLGVPAQV 504 E VR +H Q E+ G L + P+E+VGLY+PGG A PS+ LM +PA+V Sbjct: 96 ERVRIYHEKQ-KGESWSYREADGTLLGQKVTPLERVGLYVPGGKAAYPSSVLMNALPAKV 154 Query: 505 AQCKEIVFASPPRKSDGKVSPEVVYVAEKVGASKIVLAGGAQAVAAMAYGTETIPKVDKI 564 A E++ P G+++ V+ A G ++ GGAQAVAA+AYGT +P VDK+ Sbjct: 155 AGVSELIMVVPT--PGGELNELVLAAAHICGVDRVFAIGGAQAVAALAYGTGLVPPVDKV 212 Query: 565 LGPGNQFVTAAKMYVQNDTQALCSIDMPAGPSEVLVIADEDADVDFVASDLLSQAEHGID 624 +GPGN +V AK V IDM AGPSE+LV+ D D D+VA DL SQAEH D Sbjct: 213 VGPGNIYVATAKRAVFGQV----GIDMVAGPSEILVVCDGQTDPDWVAMDLFSQAEHDED 268 Query: 625 SQVILVGVNLSEKKIQEIQDAVHNQALQLPRVDIVRKCIAH-STIVLCDGYEEALEMSNQ 683 +Q IL+ + + ++ ++ + R I+ + +++C +EA +SN Sbjct: 269 AQSILISPDADF--VARVKQSIDRLLPTMEREPIIATALKERGALIVCRDMDEACRVSNH 326 Query: 684 YAPEHLILQIANANDYVKLVDNAGSVFVGAYTPESCGDYSSGTNHTLPTYGYARQYSGAN 743 APEHL L +A+ V+ + +AG++F+G YT E GDY +G NH LPT AR S Sbjct: 327 IAPEHLELSVADPLTLVEQIQHAGAIFMGRYTSEPLGDYCAGPNHVLPTSRTARFSSPLG 386 Query: 744 TATFQKFITAQNITPEGLENIGRAVMCVAKKEGLDGHRNAVKIRM 788 FQK + ++ G + +GR +A+ EGL H + + R+ Sbjct: 387 VYDFQKRSSLIMVSDAGADTLGRTASILARGEGLTAHARSAEYRL 431 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: 723 Number of extensions: 40 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: 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