Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate Ac3H11_1507 Homoserine dehydrogenase (EC 1.1.1.3)
Query= SwissProt::Q5F8J4 (435 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1507 Length = 444 Score = 487 bits (1254), Expect = e-142 Identities = 257/444 (57%), Positives = 321/444 (72%), Gaps = 10/444 (2%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAA-F 59 MKP+ +GLLG+GTVG G VL N +EISRR GR I I+ + DL E+A+ + Sbjct: 1 MKPIQVGLLGIGTVGSGVFNVLARNQDEISRRAGRGIEITMVADLDVERAKAVVGEGIQV 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 V D ++A D+D+V+EL GG GIA+ VL+AI GKH+VTANK LLA +G EIF A Sbjct: 61 VNDARAIIANPDIDIVIELIGGYGIARALVLEAIAAGKHVVTANKALLAVHGTEIFAAAS 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 + V+V FEAAVAGGIPIIKALREGL ANRI+ +AGIINGT+NFILSEMR KG F VL Sbjct: 121 AKGVMVAFEAAVAGGIPIIKALREGLTANRIQWLAGIINGTTNFILSEMRSKGLDFDVVL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 KEAQ LGYAEADPTFDIEG DA HK+T+MSA+AFG P+ F Y+EGI+KL + DIKYAE Sbjct: 181 KEAQRLGYAEADPTFDIEGVDAAHKVTLMSAIAFGIPVQFDKAYVEGITKLGAADIKYAE 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 +LGYRIKLLG+T++ KGIELRVHP+L+P RL+ANV+G MNAV V D VG TLYYG G Sbjct: 241 QLGYRIKLLGITKRADKGIELRVHPSLVPSKRLIANVEGAMNAVVVQGDAVGTTLYYGKG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQ----TILPMDEITSSYYL 355 AG+ PTASAV+AD++DIARL AD HRVPHLAFQ +Q +LPM E+ +SYYL Sbjct: 301 AGSEPTASAVIADLVDIARLHTADPEHRVPHLAFQSNTLQGAMDQLPVLPMSEVVTSYYL 360 Query: 356 RVQAKDEPGTLGQIAALLAQENVSIEALIQK-----GVIDQTTAEIVILTHSTVEKHIKS 410 R++ D+ G L ++ LLA+ VSI+A++Q+ G T +++ILTH T E + + Sbjct: 361 RLRVADQAGVLAKVTGLLAEAGVSIDAVLQREADEVGGEGSTQTDLIILTHDTREGTMDA 420 Query: 411 AIAAIEALDCVEKPITMIRMESLH 434 IA ++AL V PIT IR E L+ Sbjct: 421 VIAQMQALPTVLAPITRIRKEELN 444 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: 517 Number of extensions: 14 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: 444 Length adjustment: 32 Effective length of query: 403 Effective length of database: 412 Effective search space: 166036 Effective search space used: 166036 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 09 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