Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_074201259.1 BUQ81_RS04880 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_900141795.1:WP_074201259.1 Length = 434 Score = 436 bits (1120), Expect = e-127 Identities = 228/435 (52%), Positives = 309/435 (71%), Gaps = 4/435 (0%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQI-CPSAAF 59 MK + +GL+GLGTVGGG A+LRD+A+ + +R+ I +S + K R + S Sbjct: 1 MKTIKLGLIGLGTVGGGTLAILRDSADLLQQRVNANIEVSIIAVRDLNKPRAVDTGSIQL 60 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 DP ++V DVD+VVEL GGTG+A+E VL+AI+NGKH+VTANK LLAE+G+E+F AE Sbjct: 61 TDDPTQVVNHPDVDIVVELMGGTGLARELVLRAIDNGKHVVTANKALLAEHGDEVFAAAE 120 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 KQ V V +EAA AGGIPIIKALREGL+AN I +AGIINGT N+IL+EM++ G+ F VL Sbjct: 121 KQGVQVAYEAAAAGGIPIIKALREGLSANNIDWVAGIINGTGNYILTEMKQPGADFNAVL 180 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 K AQ LGYAEADPTFD+EG DA HK+TI+++LAFG P+ F Y EGIS++ + D+++A+ Sbjct: 181 KRAQELGYAEADPTFDVEGIDAAHKLTILASLAFGIPLQFEKVYTEGISRISADDMRFAD 240 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 LGY IK LG+ R+T G+ +RVHPTLIP+S LLANV GVMNAV + D VG TLYYG G Sbjct: 241 MLGYEIKHLGIARRTDDGVSMRVHPTLIPKSVLLANVSGVMNAVMTHGDHVGPTLYYGPG 300 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AGA PTASAVVADI+D+ R ++ RVP L F+ + ++ M+ + + YLR A Sbjct: 301 AGAGPTASAVVADIVDVVRALDCAPDARVPALGFR--TTRDLPVMDMEAVQCAAYLRFLA 358 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVIDQT-TAEIVILTHSTVEKHIKSAIAAIEAL 418 KD PG L + + +LA++ +SIE + Q+ D + A +V++T+ E + +AIAA+EAL Sbjct: 359 KDAPGVLARFSTVLAEQGISIEHMHQEPCDDGSGDALVVLITNEVPESAMNTAIAALEAL 418 Query: 419 DCVEKPITMIRMESL 433 ++ + IR+ESL Sbjct: 419 PEIDGTVQRIRIESL 433 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: 474 Number of extensions: 11 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: 434 Length adjustment: 32 Effective length of query: 403 Effective length of database: 402 Effective search space: 162006 Effective search space used: 162006 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