Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_012282995.1 HM1_RS08710 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_000019165.1:WP_012282995.1 Length = 429 Score = 421 bits (1082), Expect = e-122 Identities = 221/426 (51%), Positives = 301/426 (70%), Gaps = 1/426 (0%) Query: 2 EAIQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQLT 61 + I VGLLGLGTVG G ++I++N + + ++G PV+VKK+LV++L+K R V VDPA LT Sbjct: 3 QPIMVGLLGLGTVGGGTLRILQNRVEDIAQRLGRPVQVKKVLVRNLHKPRPVVVDPALLT 62 Query: 62 TNADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAASA 121 N DIL+DP+I +V+E+MGGI +Y+ AL K+VVTANKDLMAV+G EL A A Sbjct: 63 DNPADILEDPEISIVVELMGGIHPALDYIKSALKAGKNVVTANKDLMAVHGRELFDLAEA 122 Query: 122 NGCDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVLK 181 DL +EASVAGGIPI+R L LA++RI ++ GI+NGTTN+ILTKM++ G + EVLK Sbjct: 123 KELDLEFEASVAGGIPIIRPLKVCLAANRIEELKGIINGTTNFILTKMTQEGSDFGEVLK 182 Query: 182 EAQELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGKQ 241 EAQ LGYAEADP +DVEGLDAARK+AI+A++ F+ +I L+DV VEGIT++T DIQY +Q Sbjct: 183 EAQALGYAEADPTADVEGLDAARKLAIVASIAFNSRITLNDVYVEGITKVTARDIQYARQ 242 Query: 242 LGYTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPGA 301 +GYT+KL+GIA KVE V P ++ D HPLA+VND +NA++V G+AVGETMFYG GA Sbjct: 243 MGYTIKLLGIAKEIDGKVEARVHPAMIPDCHPLAAVNDAFNAIFVKGDAVGETMFYGRGA 302 Query: 302 GSLPTATAVVSDLVGVMKNMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEVGV 361 G +PT +AVV D++ V +N+ G G + T +QK ++ EI K+FLRL V ++ GV Sbjct: 303 GDMPTGSAVVGDIIDVARNIIKGHTGRISCTCYHQKPVRPIGEIVCKYFLRLVVTEKPGV 362 Query: 362 FANITSIFSEHSVSFEKILQMPLKENGLAEIVLVTHQASLQDYEDILVKLRDLNAVHEIK 421 A I +F + VS + ++Q + AEIVLVTH + + L L D+ +V + Sbjct: 363 LAAIAGVFGDQGVSIQTLIQQETIGDS-AEIVLVTHPVREDNLQMALKILSDMPSVERVG 421 Query: 422 SSYRVE 427 + RVE Sbjct: 422 NVIRVE 427 Lambda K H 0.316 0.134 0.368 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: 480 Number of extensions: 16 Number of successful extensions: 2 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: 432 Length of database: 429 Length adjustment: 32 Effective length of query: 400 Effective length of database: 397 Effective search space: 158800 Effective search space used: 158800 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: 41 (21.6 bits) S2: 51 (24.3 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