Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_015799204.1 AFER_RS09360 homoserine dehydrogenase
Query= BRENDA::Q56R01 (433 letters) >NCBI__GCF_000023265.1:WP_015799204.1 Length = 425 Score = 327 bits (839), Expect = 3e-94 Identities = 197/429 (45%), Positives = 259/429 (60%), Gaps = 10/429 (2%) Query: 7 LKVALLGCGVVGSEVARIMTTHGDDHAARIGAPVELAGVAVRRPSKVR-AGIPQELITTD 65 ++VALLGCGVVGS + R++ R+G P+EL + VR + R A +P L+T D Sbjct: 1 MRVALLGCGVVGSSLVRLLDRDAALLERRLGEPIELTSIVVRDIQRPRDAWVPMGLVTDD 60 Query: 66 ATALVKRGDIDVVIEVIGGIEPARTLITTAFEHGASVVSANKALLAEDGATLYAAAERHG 125 A + +D+V+E++G + A + A G +VV+ANK +LA+ L AE G Sbjct: 61 LDAAITDPSVDIVVELMGQPKVALLALERALLAGKAVVTANKDVLADHLGRLERLAEASG 120 Query: 126 RDLYFEAAVAGAIPLIRPLRESSPGNKVNRVLGIVNGTTNFILDRMDSSGAGYTEALDEA 185 DL FEAAVAG +PLIR LR S G ++ + GIVNGT+NF+L RM +GA EA+ EA Sbjct: 121 VDLLFEAAVAGGVPLIRVLRTSLFGERLWSLQGIVNGTSNFVLTRMSETGAELAEAVAEA 180 Query: 186 TALGYAEADPTADVEGFDAAAKAAILAGIAFHTRVRLDDVHREGLTEVTAADMASARRMG 245 LGYAEADP+ D++G DAAAKAAILA +AF VR D V EG+ VTAAD+ A G Sbjct: 181 ERLGYAEADPSRDLDGRDAAAKAAILASLAFERSVRADHVRTEGIVGVTAADVRFAHASG 240 Query: 246 CTVKLLAICER--AADGRSVTARVHPAMIPLSHPLASVREAYNAVFVESEAAGQLMFYGP 303 +KLLA R ADG +++ V PA++P HPLA VR+A NA+FVE +A G+L+F GP Sbjct: 241 SEIKLLATARRLDEADGEALSVEVFPALVPREHPLAGVRDAANAIFVEGQAVGELVFIGP 300 Query: 304 GAGGAPTASAVLGDLVAVCRNKLAG--ATGPGESAYTQLPVSPMGEVVTRYHISLDVADK 361 GAGG PTA+AVL D++ +N+ AG +T P T L G + R+ ISL V D Sbjct: 301 GAGGLPTAAAVLADILEAAQNRRAGRRSTAPAREEPTMLSA---GSITGRFAISLLVRDA 357 Query: 362 PGVLAQVATVFAEHGVSIDTVRQQGRQDSSGEASLVVVTHRAPDAALQGTVEALRSLDTV 421 GVLA+VA VF E GVSI V Q G G A L++VTH A ++ L +L V Sbjct: 358 AGVLARVAEVFGEEGVSIAQVEQLGA--GEGHAHLMLVTHEATLEQMEAIDRQLVTLGDV 415 Query: 422 RGVASIMRV 430 G RV Sbjct: 416 VGRRQRYRV 424 Lambda K H 0.317 0.132 0.371 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: 425 Number of extensions: 19 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: 433 Length of database: 425 Length adjustment: 32 Effective length of query: 401 Effective length of database: 393 Effective search space: 157593 Effective search space used: 157593 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