Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_009544945.1 CCE_RS11165 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_000017845.1:WP_009544945.1 Length = 432 Score = 333 bits (854), Expect = 6e-96 Identities = 181/432 (41%), Positives = 284/432 (65%), Gaps = 12/432 (2%) Query: 4 IQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQLTTN 63 +++GLLGLGTVG+G +I+ + + + + + + K+ V+ L+K R V + P +TT+ Sbjct: 3 VKIGLLGLGTVGTGTAQILLDPTGR--NPLLQDINISKVGVRSLDKPRQVQLAPGVITTD 60 Query: 64 ADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAASANG 123 + ++ DP+I +V+E++GGIE R+ +L+A+++KKHVVTANK ++A +G E+ +AA+ G Sbjct: 61 LETVVNDPEIAIVVELLGGIEPARSLILQAIAQKKHVVTANKAVIARHGDEIYSAANEAG 120 Query: 124 CDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVLKEA 183 + EA+V GGIPI++ L L ++RI+ ++GIVNGTTNYILTKM+ G + EVL EA Sbjct: 121 VYVLLEAAVGGGIPIIKPLKQSLGANRISSIIGIVNGTTNYILTKMTSAGADFAEVLTEA 180 Query: 184 QELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGKQLG 243 Q+LGYAEADP +DV+GLDAA K+AILA+LGF ++ +DV EGI +++ DI Y QLG Sbjct: 181 QQLGYAEADPTADVDGLDAADKIAILASLGFGGRVKREDVYCEGIRQVSAADITYADQLG 240 Query: 244 YTMKLIGIAH-REG---EKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGP 299 + +KL+ IA EG E++++ V PTL+ HPLA++N NAV V G +G+ MF+GP Sbjct: 241 FVIKLLAIAKGAEGEISEQLQLRVHPTLVPKDHPLANINGVSNAVLVEGSPLGQVMFFGP 300 Query: 300 GAGSLPTATAVVSDLVGVM-----KNMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLH 354 GAG+ PTA+AVVSD++ ++ + ++ + Q+ ++ + I ++F+ R Sbjct: 301 GAGAGPTASAVVSDIMNIVAILKSSGLTTTLDPLLSCVHQHFCQITPIEAINTRFYARFL 360 Query: 355 VKDEVGVFANITSIFSEHSVSFEKILQMPLKENGLAEIVLVTHQASLQDYEDILVKLRDL 414 KD GV ++ + F H VS E ++Q+ + LAEIV+VTH ++ L ++R L Sbjct: 361 TKDLPGVIGHLGTTFGNHQVSLESVVQIGF-QGELAEIVVVTHYVCEGNFRTALDEIRTL 419 Query: 415 NAVHEIKSSYRV 426 A+ I S RV Sbjct: 420 EAIDSIPSILRV 431 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: 473 Number of extensions: 25 Number of successful extensions: 4 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: 432 Length adjustment: 32 Effective length of query: 400 Effective length of database: 400 Effective search space: 160000 Effective search space used: 160000 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 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