Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_014449304.1 LFE_RS05785 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000284315.1:WP_014449304.1 Length = 440 Score = 360 bits (924), Expect = e-104 Identities = 188/435 (43%), Positives = 274/435 (62%), Gaps = 1/435 (0%) Query: 2 KPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSA-AFV 60 KPV IGL+G GTVG G + E + +RLG + +S++ D S + S Sbjct: 6 KPVVIGLIGAGTVGSGLIQLFLREKELLEQRLGFPLVLSSIADRSIHSLKMDGLSQFKLT 65 Query: 61 KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEK 120 DP ++++ +V +V+EL GG AK +L AI GK +VTANK LLA +G E+F Sbjct: 66 TDPMDVISDPEVQIVIELIGGIEPAKTFLLDAINRGKSVVTANKALLALHGEELFSAVRT 125 Query: 121 QNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLK 180 V + FE AV GGIPI++ALREG+ +R+ S+ GIINGTSN+IL++M E +F++ L Sbjct: 126 HGVDIAFEGAVCGGIPILRALREGIGGDRVLSLKGIINGTSNYILTKMTEDRISFSEALS 185 Query: 181 EAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEE 240 +AQ+LGYAEADPTFD++G DA HK+ I+ L+FG P+ FS ++GI ++ DI++ E Sbjct: 186 QAQSLGYAEADPTFDVDGMDAAHKLAILGTLSFGVPIPFSEIPVDGIRGINELDIEFGRE 245 Query: 241 LGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGA 300 LGY +KLLG+ + G ++LRVHP +PE LLA VDGV NAV V +G L+YG GA Sbjct: 246 LGYVLKLLGIAKDHGTSVDLRVHPAFLPEESLLAKVDGVFNAVEVTGRALGTALFYGRGA 305 Query: 301 GALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAK 360 GA PTASAV+ DI+++AR + ++ +VP L F + + P E+ S YYLR A Sbjct: 306 GADPTASAVMGDILELARGIHSECTLQVPPLGFSWDARHPRPMTPRSEVKSEYYLRFMAH 365 Query: 361 DEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALDC 420 D PGTL ++ +L + +SIE++IQKG + +VILT++ + I+SA+ I+ Sbjct: 366 DRPGTLSFLSGILGEHGISIESVIQKGRKKGGSVPVVILTYTATQASIQSALEIIDHSHH 425 Query: 421 VEKPITMIRMESLHD 435 V +P +I +E + + Sbjct: 426 VTEPTVLIHVERVSE 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: 432 Number of extensions: 15 Number of successful extensions: 2 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 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