Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate Synpcc7942_2090 Synpcc7942_2090 homoserine dehydrogenase
Query= BRENDA::Q56R01 (433 letters) >FitnessBrowser__SynE:Synpcc7942_2090 Length = 445 Score = 325 bits (834), Expect = 1e-93 Identities = 183/433 (42%), Positives = 271/433 (62%), Gaps = 15/433 (3%) Query: 8 KVALLGCGVVGSEVARIMTTHGDDHAARIGAPVELAGVAVRRPSKVRA-GIPQELITTDA 66 KV LLG G VG+ A+I+ D + +EL V VR K R+ I ++ +TTD Sbjct: 17 KVGLLGLGTVGTGTAQILLDPADRQP--LLQELELYRVGVRSLDKPRSVDISRDRLTTDL 74 Query: 67 TALVKRGDIDVVIEVIGGIEPARTLITTAFEHGASVVSANKALLAEDGATLYAAAERHGR 126 ++V+ +D+V+E++GG+EP+R+LI TA HG VV+ANKA++A G ++AAA G Sbjct: 75 ESIVRDPAVDIVVELLGGLEPSRSLILTAIAHGKHVVTANKAVIARYGEEIFAAAADAGV 134 Query: 127 DLYFEAAVAGAIPLIRPLRESSPGNKVNRVLGIVNGTTNFILDRMDSSGAGYTEALDEAT 186 + EAAV G IP+I PL++S N++ +LGI+NGTTN+IL RM G + L +A Sbjct: 135 YVLLEAAVGGGIPVIEPLKQSLCANRIQGILGIINGTTNYILTRMQREGGDFGPILADAQ 194 Query: 187 ALGYAEADPTADVEGFDAAAKAAILAGIAFHTRVRLDDVHREGLTEVTAADMASARRMGC 246 LGYAEADPTADV+G+DAA K AILA +AF RV + EG+ +TA+D+A A +G Sbjct: 195 RLGYAEADPTADVDGWDAADKIAILASLAFGGRVERSQITCEGIRAITASDIAYAEGLGF 254 Query: 247 TVKLLAICERAADGRS--VTARVHPAMIPLSHPLASVREAYNAVFVESEAAGQLMFYGPG 304 T+KLLA +R G + + A V+P ++PLSHPLASV + YNA+ VE + GQ+MF+GPG Sbjct: 255 TIKLLAKAKRQHQGDTWRLEASVYPTLVPLSHPLASVNDVYNAILVEGDPVGQVMFFGPG 314 Query: 305 AGGAPTASAVLGDLVAVCRNKLAGATGPG-----ESAYTQ-LPVSPMGEVVTRYHISLDV 358 AG PTASAV+ D++ + AG+ Y Q + ++P E R+++ + V Sbjct: 315 AGAGPTASAVVADILNIAAVLSAGSDRDHLDPLLACRYLQTVELAPAAETAARFYLRIVV 374 Query: 359 ADKPGVLAQVATVFAEHGVSIDTVRQQGRQDSSGE-ASLVVVTHRAPDAALQGTVEALRS 417 D PGV+ +V T+F E G+S++++ Q D SGE A LVV+TH + ++ + L + Sbjct: 375 QDSPGVIGKVGTIFGEQGISLESIVQ---TDVSGETAELVVITHEVQEGIMRQAITQLEA 431 Query: 418 LDTVRGVASIMRV 430 L V+ +A+++ V Sbjct: 432 LPLVQAIANLLHV 444 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: 443 Number of extensions: 23 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: 445 Length adjustment: 32 Effective length of query: 401 Effective length of database: 413 Effective search space: 165613 Effective search space used: 165613 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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