Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_009567245.1 AFE_RS02235 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000021485.1:WP_009567245.1 Length = 440 Score = 457 bits (1177), Expect = e-133 Identities = 234/433 (54%), Positives = 309/433 (71%) Query: 1 MKPVNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLSEEKARQICPSAAFV 60 + PV IG+LG+GTVG G VL NAEEI+RR+GRE+R+ + + + A Sbjct: 5 LAPVRIGILGMGTVGQGTVRVLERNAEEITRRVGRELRVVHAAVRNPARLEGLGLDARIS 64 Query: 61 KDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAEK 120 DP+ +V +VDVVVE+ GG A ++ AI GKH+VTANK LLAE+GNEIF A+ Sbjct: 65 SDPWAVVRDPEVDVVVEVMGGQEPALSLLMAAIAAGKHVVTANKALLAEHGNEIFAAAQA 124 Query: 121 QNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVLK 180 + V+V FEAAVAG IPIIKA+REGLA NRI+ +AGIINGTSN+ILS+M +G F L Sbjct: 125 RGVMVAFEAAVAGAIPIIKAIREGLAGNRIQWLAGIINGTSNYILSQMFREGWDFQQALA 184 Query: 181 EAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAEE 240 EAQ LGYAEADP D++G DA HKIT+M+++AFG P++F+ C++EGI L+ D+ YA E Sbjct: 185 EAQRLGYAEADPGLDVDGGDAAHKITLMASIAFGIPVDFAHCHVEGIRALERTDVVYAAE 244 Query: 241 LGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAGA 300 LGYRIKLLG+ R+ G+ELRVHPTLIP S LLANV+G NA+ V +D G++LYYG GA Sbjct: 245 LGYRIKLLGIARRRADGVELRVHPTLIPHSHLLANVEGPFNAILVESDAAGQSLYYGRGA 304 Query: 301 GALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQAK 360 G PTASAVVAD++D+AR + AD ++RVPHLAFQP + A +LPM E+ S+YYLR+ A Sbjct: 305 GGDPTASAVVADLVDVARTMTADPSNRVPHLAFQPDAMSALPLLPMAEVESAYYLRIHAH 364 Query: 361 DEPGTLGQIAALLAQENVSIEALIQKGVIDQTTAEIVILTHSTVEKHIKSAIAAIEALDC 420 + G L Q+A +LA+ +SIEAL+QK + + IV+L H E ++ AIA +EAL Sbjct: 365 NRAGVLAQVATMLAEYEISIEALVQKETPEADSVPIVLLLHRCREGDLEQAIARMEALPV 424 Query: 421 VEKPITMIRMESL 433 V +P+ +R+ESL Sbjct: 425 VVQPVLRLRVESL 437 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: 506 Number of extensions: 17 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