Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (characterized)
to candidate WP_057508710.1 ABB28_RS11205 homoserine dehydrogenase
Query= SwissProt::Q5B998 (368 letters) >NCBI__GCF_001431535.1:WP_057508710.1 Length = 362 Score = 189 bits (479), Expect = 1e-52 Identities = 131/370 (35%), Positives = 204/370 (55%), Gaps = 28/370 (7%) Query: 2 SAPIYLGVIGVGGVGTAFLNQLARLPNA----PKLILLARSSQTLLSPTPSYSPTIPAAE 57 +AP L ++G G VGTAF+ + L + P+ LA S L +P P Sbjct: 11 AAPRRLALLGTGTVGTAFVARYRALQSRGLALPRFDWLANSRAVLACDG---APEQPLHA 67 Query: 58 WKTAVETPSLTKSGALTPDEIATYLASAPGRSILVDNTSDPALASNYPVFLRKGISVVTP 117 + A P L + A P + A L + ++VD T+ +A+ + +L +G+ VVT Sbjct: 68 LRRA---PRLGDAAA--PWKQADSLHAG---DVVVDATASETVAAEHAHWLARGVHVVTA 119 Query: 118 NKKGFSSDLSLWKEIFAAAAEGKALVYHESTVGAGLPVISTLKDLVNTGDEVTRIEGVFS 177 NK G + +I A A+ A +TVGAGLP++S+L+ LV GD + RIEGV S Sbjct: 120 NKLGQGAHAQRAVQIAAHCADSGARYGDSATVGAGLPLLSSLRALVEGGDRILRIEGVLS 179 Query: 178 GTLSFLFNTFAPASGSSSAKWSEVVSQAKELGYTEPDPRDDLNGMDVARKLTILARIAGL 237 G+L++LF+ + S +S V +A + G+TEPDPR DL+G DV RKL ILAR +GL Sbjct: 180 GSLAWLFHRY-----DGSQPFSLAVREALDAGFTEPDPRLDLSGEDVRRKLLILARASGL 234 Query: 238 DVQSPDSFPIESLIPAELTSLPSSADGIAQFMARLPEFDSQMAAIKEGAEKAGKVVRYVG 297 D+ + ++SL+PA L +LP AQ + +L + D+ + A +AG+V+R++G Sbjct: 235 DL-ADGQVQVDSLVPAALATLPH-----AQALEQLAQLDAPLHQRWLRAREAGQVLRFIG 288 Query: 298 SVDVAKKEVRVGLQQFDKDSAIAGLKGSDNIISFYTRRYGSNPLIVQGAGAGGDVTAMGV 357 V+ RVG+Q D +A G+DN ++ ++ RY PL++QG GAG +VTA + Sbjct: 289 CVEAG--AARVGVQSLAADHPLASGAGTDNRVAIHSDRYRDQPLLIQGPGAGAEVTAAAL 346 Query: 358 TADLLKVIER 367 D+L++ + Sbjct: 347 LDDVLRIARK 356 Lambda K H 0.314 0.132 0.368 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: 285 Number of extensions: 14 Number of successful extensions: 5 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: 368 Length of database: 362 Length adjustment: 30 Effective length of query: 338 Effective length of database: 332 Effective search space: 112216 Effective search space used: 112216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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