Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (characterized)
to candidate WP_027490863.1 LRK54_RS05300 homoserine dehydrogenase
Query= SwissProt::Q5B998 (368 letters) >NCBI__GCF_021560695.1:WP_027490863.1 Length = 360 Score = 190 bits (483), Expect = 5e-53 Identities = 135/367 (36%), Positives = 198/367 (53%), Gaps = 32/367 (8%) Query: 2 SAPIYLGVIGVGGVGTAFLNQL-ARLPNAPKLILLARSSQTLLSPTPSYSPTIPAAEWKT 60 S+ I + ++G G VG A L L + +L+ A S + P + Sbjct: 17 SSAIAIVLLGTGVVGGALLKLLNTSAAGSLRLVGAANSRRQQTDPLSLAQRNL------- 69 Query: 61 AVETPSLTKSGALTPDEIATYLASAPGRS----ILVDNTSDPALASNYPVFLRKGISVVT 116 L + GA P + A+ LA+ G + ++VD T+ LA+ + +L +G VVT Sbjct: 70 ---REQLNQHGA--PRDNASLLAALDGSAAAVKVIVDATASTVLAARHAEWLARGYHVVT 124 Query: 117 PNKKGFSSDLSLWKEIFAAAAEGKALVYHES-TVGAGLPVISTLKDLVNTGDEVTRIEGV 175 NK +LS W+ + AA A G Y +S TVGAGLPV+STL+ L GD + +EGV Sbjct: 125 ANKALAGGELSGWRALQAALANGGR--YGDSATVGAGLPVLSTLRRLRRCGDGLLTLEGV 182 Query: 176 FSGTLSFLFNTFAPASGSSSAKWSEVVSQAKELGYTEPDPRDDLNGMDVARKLTILARIA 235 FSG+LS+LFN + S +SE++ +A++LGYTEPDPR DL+G DVARKL I+AR A Sbjct: 183 FSGSLSWLFNQY-----DGSRPFSELLREARQLGYTEPDPRSDLSGEDVARKLLIIARNA 237 Query: 236 GLDVQSPDSFPIESLIPAELTSLPSSADGIAQFMARLPEFDSQMAAIKEGAEKAGKVVRY 295 G + D ++ L+P L L + A F+ RL E D+ +AA A G V+R+ Sbjct: 238 GFAL-GTDEVQVDGLVPEALRGLSTEA-----FLTRLEELDAPLAARHAAASSRGCVLRF 291 Query: 296 VGSVDVAKKEVRVGLQQFDKDSAIAGLKGSDNIISFYTRRYGSNPLIVQGAGAGGDVTAM 355 + ++ + RVGL + A L G+DN + T RY + PL++QG GAG +VTA Sbjct: 292 LARLN-QRGHARVGLAEVPLTHPAARLYGTDNQFALTTTRYHAQPLVIQGPGAGPEVTAQ 350 Query: 356 GVTADLL 362 + D+L Sbjct: 351 ALLGDVL 357 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: 279 Number of extensions: 11 Number of successful extensions: 4 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: 360 Length adjustment: 29 Effective length of query: 339 Effective length of database: 331 Effective search space: 112209 Effective search space used: 112209 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