Align Homoserine dehydrogenase; HDH; EC 1.1.1.3 (characterized)
to candidate N515DRAFT_0577 N515DRAFT_0577 homoserine dehydrogenase
Query= SwissProt::Q5B998 (368 letters) >FitnessBrowser__Dyella79:N515DRAFT_0577 Length = 382 Score = 218 bits (554), Expect = 3e-61 Identities = 151/373 (40%), Positives = 212/373 (56%), Gaps = 37/373 (9%) Query: 7 LGVIGVGGVGTAFLNQLARLPNAPKLILLARSSQTLLSPTPSYSPTIPAAEWKTA---VE 63 +G+IG G VG+A L QL R++QT LS + A K + Sbjct: 32 VGLIGPGRVGSALLTQL-------------RAAQTRLSESGLELKLCGVAASKRMWLDCD 78 Query: 64 TPSLTK----SGALTPDEI---ATYLASAPGR-SILVDNTSDPALASNYPVFLRKGISVV 115 P L + + P ++ A ++ GR ++L+D +++ +A++Y +L +G+ VV Sbjct: 79 DPDLNRRCDRAQIWRPADLRQFARHVLGDDGRHALLIDCSANDEVAAHYAGWLAEGVHVV 138 Query: 116 TPNKKGFSSDLSLWKEIFAAAAEGKALVYHESTVGAGLPVISTLKDLVNTGDEVTRIEGV 175 TPNK S L W+ I AA+ G Y E+TV AGLPV+ TL+DL++TGDE+ ++G+ Sbjct: 139 TPNKLAGSGPLERWQAIRAASHAGARFRY-EATVCAGLPVVQTLRDLLDTGDELLAVDGM 197 Query: 176 FSGTLSFLFNTFAPASGSSSAKWSEVVSQAKELGYTEPDPRDDLNGMDVARKLTILARIA 235 FSGTL++L N +S +V +A LGYTEPDPRDDL+G+DVARKL ILAR A Sbjct: 198 FSGTLAWLCNRH-----DGGRPFSALVREAHALGYTEPDPRDDLSGLDVARKLVILAREA 252 Query: 236 GLDVQSPDSFPIESLIPAELTSLPSSADGIAQFMARLPEFDSQMAAIKEGAEKAGKVVRY 295 G + S D ++SL+PAEL +L + A FMARL E D+ MAA A G V+R+ Sbjct: 253 GWAL-SLDDVDVQSLVPAELAALDADA-----FMARLDELDAPMAAQLAIARAEGGVLRH 306 Query: 296 VGSVDVAKKEVRVGLQQFDKDSAIAGLKGSDNIISFYTRRYGSNPLIVQGAGAGGDVTAM 355 V S+D V L A + +DN++ F TRRY NPL+VQG GAG +VTA Sbjct: 307 VASLD-RDGRASVKLAVLPASHPFAHTRLTDNVVQFTTRRYHDNPLLVQGPGAGPEVTAA 365 Query: 356 GVTADLLKVIERL 368 GV DLL++ E L Sbjct: 366 GVFGDLLRIAESL 378 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: 330 Number of extensions: 18 Number of successful extensions: 6 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: 382 Length adjustment: 30 Effective length of query: 338 Effective length of database: 352 Effective search space: 118976 Effective search space used: 118976 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: 50 (23.9 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