Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_068166387.1 HTA01S_RS00735 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_001592305.1:WP_068166387.1 Length = 440 Score = 493 bits (1268), Expect = e-144 Identities = 255/440 (57%), Positives = 323/440 (73%), Gaps = 6/440 (1%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQIC-PSAAF 59 MKP+ +GLLG+GTVG G VL+ N EEI RR GR I I+ + DL +A+ I P+ Sbjct: 1 MKPIQVGLLGIGTVGSGTFNVLQRNQEEIRRRAGRGIEITMVADLDVARAQSIVGPNVKV 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 V D ++A ++D+V+EL GG GIAK V++AI GKH+VTANK LLA +G EIF A Sbjct: 61 VNDARAVIANPEIDIVIELIGGYGIAKALVMEAIAAGKHVVTANKALLAVHGTEIFAAAS 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 + V+V FEAAVAGGIPIIKALREGL AN I+ IAGIINGT+NFILSEMR+KG F VL Sbjct: 121 AKGVMVAFEAAVAGGIPIIKALREGLTANSIQWIAGIINGTTNFILSEMRDKGLDFDVVL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 KEAQ LGYAEADPTFDIEG DA HK+T+MSA+AFG P+ F Y+EGI++L + DIKYAE Sbjct: 181 KEAQRLGYAEADPTFDIEGVDAAHKVTLMSAIAFGIPVQFDKAYVEGITQLGATDIKYAE 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 +LGYRIKLLG+T++T KGIELRVHP+L+P RL+ANV+G MNAV V D VG TLYYG G Sbjct: 241 QLGYRIKLLGITKRTDKGIELRVHPSLVPSKRLIANVEGAMNAVVVQGDAVGTTLYYGKG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AG+ PTASAV+AD++DI RL AD HRVPHLAFQP ++ ++LPM E+ +SYYLR++ Sbjct: 301 AGSEPTASAVIADLVDITRLHTADPLHRVPHLAFQPDKMSDLSVLPMSEVVTSYYLRLRV 360 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQK-----GVIDQTTAEIVILTHSTVEKHIKSAIAA 414 DE G L ++ LLA +SI+A++Q+ G T+ +++ILTH T E + +A Sbjct: 361 ADEAGVLAKVTGLLANAGISIDAVLQREADEVGGEGATSTDLIILTHDTREGTMNEVLAQ 420 Query: 415 IEALDCVEKPITMIRMESLH 434 ++AL V PIT IR E L+ Sbjct: 421 MQALPSVLAPITRIRKEELN 440 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: 490 Number of extensions: 13 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: 440 Length adjustment: 32 Effective length of query: 403 Effective length of database: 408 Effective search space: 164424 Effective search space used: 164424 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 Jul 25 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