Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_011373518.1 SUDEN_RS09885 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000012965.1:WP_011373518.1 Length = 420 Score = 335 bits (860), Expect = 1e-96 Identities = 189/429 (44%), Positives = 275/429 (64%), Gaps = 13/429 (3%) Query: 4 VNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISA--MCDLSEEKARQICPSAAFVK 61 + +G++GLGTVG +LR+NA+ IS R G EI + + + +L++++ + V Sbjct: 2 IKVGIIGLGTVGSSVVNILRENADVISARAGVEIVVKSGVVKNLNKDRTHLGIKISDNVD 61 Query: 62 DPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEKQ 121 D ++ +++DVVVEL GG E V KA++NGK +VTANK LLA + E+ +A+ Sbjct: 62 D---ILDDEEIDVVVELMGGVEEPFEVVKKALKNGKAVVTANKALLAYHRYELADIAK-- 116 Query: 122 NVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLKE 181 ++ ++EA+VAGGIPII ALR+GL+AN I+SI GI+NGT N++L++M G A+ +LKE Sbjct: 117 DIAFEYEASVAGGIPIINALRDGLSANHIESIMGIMNGTCNYMLTKMTNDGVAYDTILKE 176 Query: 182 AQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEEL 241 AQALGYAEADPTFD+ G D HK+ I++++A+G +EGI + DI +A+E Sbjct: 177 AQALGYAEADPTFDVGGFDTAHKLLILASIAYGIDAKPEDILIEGIENISRDDIAFAKEF 236 Query: 242 GYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGAG 301 GY IKLLG+ +K +ELRVH +LI + ++A +DGVMNA+ V D VGETLYYGAGAG Sbjct: 237 GYVIKLLGIAKKDKNEVELRVHASLIKKDAMIAKIDGVMNAISVVGDKVGETLYYGAGAG 296 Query: 302 ALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAKD 361 TASAVVA+IIDIAR + P L F T+ +I S YYLR+ D Sbjct: 297 GNATASAVVANIIDIAR-----SGKSKPMLGFDKPMEGKLTLKAAGDIESKYYLRINVSD 351 Query: 362 EPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALDCV 421 + G L +I + + ++SIEA++Q+ Q +A ++I TH E I++ I++IE L+ V Sbjct: 352 KIGVLARITKIFEENSISIEAVLQRQSCTQ-SANLLISTHKAYEHDIQNLISSIEKLEFV 410 Query: 422 EKPITMIRM 430 MIR+ Sbjct: 411 NSKPVMIRI 419 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: 443 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: 435 Length of database: 420 Length adjustment: 32 Effective length of query: 403 Effective length of database: 388 Effective search space: 156364 Effective search space used: 156364 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