Align NAD(+)-dependent homoserine dehydrogenase; NAD(+)-dependent HSD; NgHSD; EC 1.1.1.3 (characterized)
to candidate WP_013450991.1 CALNI_RS04335 homoserine dehydrogenase
Query= SwissProt::Q5F8J4 (435 letters) >NCBI__GCF_000183405.1:WP_013450991.1 Length = 441 Score = 367 bits (943), Expect = e-106 Identities = 199/436 (45%), Positives = 279/436 (63%), Gaps = 7/436 (1%) Query: 4 VNIGLLGLGTVGGGAAAVLRDNAEEISRRLGREIRISAMCDLS----EEKARQICPSAAF 59 VN+G++G GTVG G VL DNA I + G +I + ++ DL +++ + P+ Sbjct: 6 VNVGIVGYGTVGKGTVNVLIDNANVIKEKTGIDIFVKSVADLKINEFDDQFLRKVPNK-- 63 Query: 60 VKDPFELVARKDVDVVVELFGGTGIAKEAVLKAIENGKHIVTANKKLLAEYGNEIFPLAE 119 D ++ +D+VVEL GG AK+ +L AIE KH+VTANK LLA YG EIF AE Sbjct: 64 YTDADMIINDPVIDIVVELIGGYNAAKKVILDAIEKKKHVVTANKALLAVYGTEIFKKAE 123 Query: 120 KQNVIVQFEAAVAGGIPIIKALREGLAANRIKSIAGIINGTSNFILSEMREKGSAFADVL 179 +++V + FE +V GGIPIIK L+E LAAN IK I GIINGT+N+IL+ M ++G F +VL Sbjct: 124 EKSVQLGFEGSVGGGIPIIKVLKEDLAANNIKEIYGIINGTANYILTRMEKEGKEFDEVL 183 Query: 180 KEAQALGYAEADPTFDIEGNDAGHKITIMSALAFGTPMNFSACYLEGISKLDSRDIKYAE 239 K+AQ LGYAEADPTFDIEG D HKITI+S++AF T + F ++EGIS + DI +A+ Sbjct: 184 KDAQRLGYAEADPTFDIEGIDTAHKITILSSIAFNTIIPFDKVFVEGISSIKQVDIDFAK 243 Query: 240 ELGYRIKLLGVTRKTGKGIELRVHPTLIPESRLLANVDGVMNAVRVNADMVGETLYYGAG 299 +L +IKLL + +K IE+RVHPT+IPE +L+ V+ V NA+ + +D + T++YG G Sbjct: 244 KLNCKIKLLAIAKKHENDIEVRVHPTMIPERYILSKVENVFNAIYLVSDKLDRTIHYGRG 303 Query: 300 AGALPTASAVVADIIDIARLVEADTAHRVPHLAFQPAQVQAQTILPMDEITSSYYLRVQA 359 AG LPT SAV DII IAR + RVP L F + +D+I SS+YLR A Sbjct: 304 AGGLPTGSAVAGDIISIARDIICGCHKRVPVLGFTKEYRSYFPVKNIDDIRSSFYLRFMA 363 Query: 360 KDEPGTLGQIAALLAQENVSIEALIQKGVIDQ-TTAEIVILTHSTVEKHIKSAIAAIEAL 418 D+PG L +IA +L + N+SI A IQ G +V +TH T+ +H+ A+ I+++ Sbjct: 364 LDKPGVLSKIAGVLGKYNISISAAIQPGDYSPGDVVPLVFMTHETIGRHVSDAVREIDSM 423 Query: 419 DCVEKPITMIRMESLH 434 + V+ +IR+E H Sbjct: 424 EYVKSKTVVIRVEGAH 439 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: 484 Number of extensions: 24 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: 441 Length adjustment: 32 Effective length of query: 403 Effective length of database: 409 Effective search space: 164827 Effective search space used: 164827 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