Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_012971317.1 ALVIN_RS10585 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000025485.1:WP_012971317.1 Length = 438 Score = 501 bits (1290), Expect = e-146 Identities = 264/436 (60%), Positives = 323/436 (74%), Gaps = 3/436 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRIS--AMCDLSEEKARQICPSAA 58 M+PV IGLLGLGTVGGG A VL NA EI+RR GR I I+ A + E + Sbjct: 1 MEPVKIGLLGLGTVGGGTATVLTRNAREIARRAGRGIEIARAAAREYRPELIEGLDQIGH 60 Query: 59 FVKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLA 118 D F+LV D+ +VVEL GG A E V++AIENGKH+VTANK L+A++GNEIF A Sbjct: 61 IGDDAFDLVEDPDIQIVVELIGGYSPALELVMRAIENGKHVVTANKALIAKHGNEIFAAA 120 Query: 119 EKQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADV 178 ++ V+V FEAAVAGGIPIIKALREGLAAN I+ IAGIINGT NFILSEMR+KG AFADV Sbjct: 121 REKGVMVGFEAAVAGGIPIIKALREGLAANHIEWIAGIINGTGNFILSEMRDKGRAFADV 180 Query: 179 LKEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYA 238 L EAQALGYAEADPTFD+EG DA HK+TI+ +LAFG P+ F C+ EGIS++D++D+ A Sbjct: 181 LAEAQALGYAEADPTFDVEGIDAAHKLTILGSLAFGIPLQFERCFTEGISRIDAQDVANA 240 Query: 239 EELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGA 298 ELGYRIK LG+ R++ GIELRVHPTLIPE RLLANVDGVMN V V D VG TLYYGA Sbjct: 241 AELGYRIKHLGIARRSPGGIELRVHPTLIPERRLLANVDGVMNGVLVKGDAVGPTLYYGA 300 Query: 299 GAGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQ 358 GAGALPTASAVVAD++D+ R + D +RVPHLAFQP ++ +L M+ I +SYYLR+ Sbjct: 301 GAGALPTASAVVADLVDVTRALTTDPNNRVPHLAFQPDELADTPVLAMESIETSYYLRLT 360 Query: 359 AKDEPGTLGQIAALLAQENVSIEALIQKG-VIDQTTAEIVILTHSTVEKHIKSAIAAIEA 417 A D PG + +IA++L +E +SIEA+ QK +T +V+LTH +E + +AIA IEA Sbjct: 361 ALDRPGVMARIASILGEEGISIEAIKQKAPATGETQVTLVMLTHRVIEGRMNTAIARIEA 420 Query: 418 LDCVEKPITMIRMESL 433 LD V+ + IRMESL Sbjct: 421 LDSVQGAVVRIRMESL 436 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: 510 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: 438 Length adjustment: 32 Effective length of query: 403 Effective length of database: 406 Effective search space: 163618 Effective search space used: 163618 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