Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_010529189.1 ON01_RS01235 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_000224785.1:WP_010529189.1 Length = 435 Score = 522 bits (1344), Expect = e-153 Identities = 263/431 (61%), Positives = 329/431 (76%), Gaps = 2/431 (0%) Query: 2 EAIQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDV--DPAQ 59 +++ VGLLG+G VGSGV+ +IE HQ KL HQ+GC V VK LV++ NK RDV+ + Sbjct: 3 DSVSVGLLGVGVVGSGVISLIEQHQAKLAHQLGCSVHVKSALVRNPNKVRDVNAKTNGTL 62 Query: 60 LTTNADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAA 119 LTTN DD+L DP+IDV++EVMGGIEE R +LKA KKHVVTANKDL+A+YG+EL +A Sbjct: 63 LTTNPDDVLNDPEIDVIVEVMGGIEEARESILKAFEAKKHVVTANKDLVALYGAELHDSA 122 Query: 120 SANGCDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEV 179 N CD +YEASVAGGIPILR + DG ASD I ++MGIVNGTTNYILTKM G +YE+ Sbjct: 123 GKNKCDFYYEASVAGGIPILRGITDGFASDHIEQLMGIVNGTTNYILTKMHNEGVSYEDA 182 Query: 180 LKEAQELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYG 239 LKEAQELG+AEADPA+DVEGLDAARKMAIL L FS IDLDDV+V GI I +D+QYG Sbjct: 183 LKEAQELGFAEADPAADVEGLDAARKMAILGRLAFSTHIDLDDVEVTGINGIELDDLQYG 242 Query: 240 KQLGYTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGP 299 LG+ MKLIG A +G++VEV+VQP L+S HPLA V +EYNAVYVYGEAVGE MFYG Sbjct: 243 DSLGFNMKLIGFAKFDGKQVEVNVQPALISKEHPLADVKNEYNAVYVYGEAVGEAMFYGA 302 Query: 300 GAGSLPTATAVVSDLVGVMKNMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEV 359 GAGS+PTA AV+SD+V V+KNM GV G+ V P+++K+LK D+ + +++ R H KDE Sbjct: 303 GAGSMPTAAAVISDVVTVIKNMHRGVTGSQFVEPRFKKELKTEDQRFGQYYARFHAKDEA 362 Query: 360 GVFANITSIFSEHSVSFEKILQMPLKENGLAEIVLVTHQASLQDYEDILVKLRDLNAVHE 419 GVF+ I+S+F+E +SF++ILQ PLKE AEIV++TH++SL+ L L L+ V E Sbjct: 363 GVFSRISSLFNEFDISFKQILQNPLKEADAAEIVVITHRSSLEKMHQALDALSKLDEVLE 422 Query: 420 IKSSYRVEGSA 430 KS Y+VEG A Sbjct: 423 TKSFYKVEGDA 433 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: 600 Number of extensions: 21 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: 435 Length adjustment: 32 Effective length of query: 400 Effective length of database: 403 Effective search space: 161200 Effective search space used: 161200 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 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