Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate Ac3H11_4236 Homoserine dehydrogenase (EC 1.1.1.3)
Query= SwissProt::Q5F8J4 (435 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4236 Length = 463 Score = 382 bits (981), Expect = e-110 Identities = 212/442 (47%), Positives = 286/442 (64%), Gaps = 10/442 (2%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQIC-PSAAF 59 M+P+ +G++G+GTVG G VL N I+ R GR I++ +C S +A + A Sbjct: 21 MRPLRVGMIGIGTVGAGTFRVLARNQALIAGRAGRGIKLVVVCARSLARAMSVVGKDVAL 80 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 DP ++ DVDV+VE GGTG A++ VL AI GKH+VTANK LLAE+GNEIF A Sbjct: 81 TNDPMQVATHPDVDVLVEAAGGTGPARDWVLAAIRAGKHVVTANKALLAEHGNEIFAAAR 140 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 + V V +E AVA IPI+KALREGL ANRI+ +AGIINGT+NFILS+MR++G FA+ L Sbjct: 141 QHGVAVAYEGAVAVSIPIVKALREGLTANRIEWVAGIINGTTNFILSKMRDEGVGFAEAL 200 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 +AQALGYAEADPTFDIEG DA HKI++++A AFG P+ F+ +EGI+ L D+ AE Sbjct: 201 TQAQALGYAEADPTFDIEGIDAAHKISLLAANAFGMPVRFADAQVEGITALQGLDVACAE 260 Query: 240 ELGYRIKLLGVT--RKTG--KGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLY 295 +LGYRIKLLGV RK G +G+ELRV P L+P + LLA+V+G MNAV V D G T+Y Sbjct: 261 QLGYRIKLLGVAKRRKDGDAEGVELRVQPALVPATHLLAHVNGSMNAVMVKGDASGVTMY 320 Query: 296 YGAGAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQ-TILPMDEITSSYY 354 YGAGAG+ PTASAV+AD++D+ARL A RVPHL F V +LP + + +Y Sbjct: 321 YGAGAGSEPTASAVIADLVDVARLQGTHAAQRVPHLGFHADAVNNNLAVLPRAAVHTRHY 380 Query: 355 LRVQAKDEPGTLGQIAALLAQENV---SIEALIQKGVIDQTTAEIVILTHSTVEKHIKSA 411 LRV + + + A LA + V +E +K ++++LT + + + A Sbjct: 381 LRVPV-HQAQQIEAVGAWLAAQQVPVARVELACEKAAPAGAGPQVLVLTDAVAQSTVDLA 439 Query: 412 IAAIEALDCVEKPITMIRMESL 433 + A+ A V P+ +R+E L Sbjct: 440 VHALAAHPAVAGPVAALRVEML 461 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: 475 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: 463 Length adjustment: 33 Effective length of query: 402 Effective length of database: 430 Effective search space: 172860 Effective search space used: 172860 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