Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_010936896.1 DET_RS06220 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000011905.1:WP_010936896.1 Length = 433 Score = 303 bits (776), Expect = 7e-87 Identities = 170/431 (39%), Positives = 258/431 (59%), Gaps = 9/431 (2%) Query: 4 VNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKAR---QICPSAAFV 60 + +G++GLG V G + VL + E +S +LG +++ + L ++ +R ++ P Sbjct: 6 IGVGVIGLGVVAGQVSKVLHEREEFLSAQLGFPLKLKKVKVLPQDMSRPLAKLLPEGVLT 65 Query: 61 KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEK 120 D + +D+VVE GG A + + ++ GK +VT+NK+++A++ E+ LA + Sbjct: 66 TDEDDFFNTPGLDIVVEAIGGEYPAFNLLSRGLKMGKCVVTSNKEVIAKHAPELVKLARE 125 Query: 121 QNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLK 180 N ++ EA+V GGIP+I + LAAN I I IINGT+N+IL+ M ++G F LK Sbjct: 126 NNTGLRCEASVGGGIPLISPFQYDLAANHINGIYAIINGTTNYILTRMAKEGLDFETALK 185 Query: 181 EAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEE 240 +AQ+LGYAEA+P+ DIEG DA +K+ IM+++ F + Y EGIS+L SRD YA+E Sbjct: 186 QAQSLGYAEANPSNDIEGTDAVYKLAIMASINFQCKVKPEDIYREGISRLTSRDFCYADE 245 Query: 241 LGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGA 300 LG+ IKLL +T+ IE RVHP +P+ LA VDGV NAV V D+VG L+ G GA Sbjct: 246 LGFNIKLLAITKPGNGQIEARVHPVFLPKDEWLAKVDGVFNAVLVEGDLVGPVLFQGQGA 305 Query: 301 GALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAK 360 GA T+SAVVAD++ A+ + +R+ +P V+ PM +I + YYLR+ Sbjct: 306 GASATSSAVVADVLAAAQDIHLGVGNRMRWNMDKPLGVK-----PMSDILTRYYLRMTVT 360 Query: 361 DEPGTLGQIAALLAQENVSIEALIQKGVIDQT-TAEIVILTHSTVEKHIKSAIAAIEALD 419 D PG L IA +L N+SI ++IQK ++ TAEIVI+TH E ++ A+ + LD Sbjct: 361 DSPGVLALIARVLGDHNISISSVIQKETDEENLTAEIVIMTHPAKEAFVQQALVELGGLD 420 Query: 420 CVEKPITMIRM 430 V+ +R+ Sbjct: 421 KVKDINNFVRV 431 Lambda K H 0.318 0.135 0.369 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: 390 Number of extensions: 15 Number of successful extensions: 3 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: 435 Length of database: 433 Length adjustment: 32 Effective length of query: 403 Effective length of database: 401 Effective search space: 161603 Effective search space used: 161603 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 (21.7 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