Align homoserine dehydrogenase; EC 1.1.1.3 (characterized, see rationale)
to candidate WP_085217441.1 B9N75_RS02885 homoserine dehydrogenase
Query= uniprot:A0A168MV81 (583 letters) >NCBI__GCF_900177405.1:WP_085217441.1 Length = 573 Score = 313 bits (802), Expect = 1e-89 Identities = 219/565 (38%), Positives = 303/565 (53%), Gaps = 20/565 (3%) Query: 28 EVVVLKFGSSILRSPAEAPLVASAVYGHVRAGRKVVAVVSAFGGATDRLLGEA-RALGLA 86 +V VLKFGSS+L S A+ +A Y H+RAG KVV V+SA G TD L +A R G A Sbjct: 7 DVCVLKFGSSVLESEADYRCLADEAYRHIRAGEKVVLVLSAIAGETDALFAQAERVGGDA 66 Query: 87 HSNDLLPGYVALGEEKSAALVAIACDRIGLDACALSVRELGIVAEGEPEHSRPCGLRPDH 146 + L+ +GE +SAAL+A+A RIG+ A AL E+ +VAEG P S L Sbjct: 67 AAPALVARLARIGELRSAALMALALGRIGVRAAALDPHEMALVAEGAPLDSNLVALDAAA 126 Query: 147 LKQALDRHEVVVVPGFGAVRPDGKVALLGRGGSDLTAVFLAAELGLKKVRLVKDVDGLYD 206 + L HE +VVPGF A + V LGRGG+DL+AVF AA LG K+VRL+KDVDG+Y Sbjct: 127 VAAKLADHEAIVVPGFIAGHAEHGVVTLGRGGTDLSAVFFAAALGAKRVRLLKDVDGVYA 186 Query: 207 HDPNDKTAPALRYRRASWDVARKLGGALVQHDAIDLGESRGVEIEVAALDRADGTVIGDR 266 DP A RY +D A + L+Q AI ++ G+ IE+AAL + TVI Sbjct: 187 EDP-AVNPRAERYGAIDYDTAAEASAGLIQPKAIAAAKAAGIAIEIAALGEHEATVIAAG 245 Query: 267 SAPPGPAPALPPLKVAVAGCGVVGGGVLGKL-LNDPRYEVVGVLVRNPKKARDVDCPASL 325 A PL+VA+ G G VG GV + + R+ + VLVR+ RD PA Sbjct: 246 PAIRRLPLLTAPLRVALLGHGAVGAGVAECIDRHSDRFALGKVLVRH-LDGRD---PAR- 300 Query: 326 FTSNPADLWAKKPDVVLEALSEGEAGHAVIRAALEAGCDVASANKQAVSRDPGGLQELAK 385 FT + + A PDVV+E + +A ++ AL G V +ANK V+ A Sbjct: 301 FTDDLDEALAGDPDVVIELIGGSDAAD-ILSRALRRGAHVVTANKAVVAAHYDAFHAAAT 359 Query: 386 ANGRRMFWSASVGGGSPMIETVRAARAAGEVVGFEAVLNGTVNFMLERLGDGAAFNEALA 445 A G ++ +S +VGGG+P++E A +V E V+NGT N + RL G + AL Sbjct: 360 AGGSQLVFSGAVGGGAPVLEAAARLHAGPGLVAVEGVMNGTANHLFGRLAAGWPLDRALI 419 Query: 446 DARAAGFAEEDPSSDLEGLDAAAKVRLLCHEAFGRSPDGD-VPRDHL-------TEATSA 497 +ARA GFAE DPS+D++G DAAAK+ +L FG + + +PR L +A A Sbjct: 420 EARALGFAEADPSADVDGYDAAAKLAILARACFGAALAPERIPRQSLRATTPETAQAALA 479 Query: 498 AGGV-RQIGAAH-LKDGVIRPSVSLNADHGDPLFSTLRGEGNALKVYGADGRVWRCRGRG 555 G V +Q+G L +G + V++ + + G N ++ GRV G+G Sbjct: 480 RGEVLKQVGRCRVLPNGTLAAGVTIESLPLAHPLAGANGAENRFRLTDRAGRVHTIFGQG 539 Query: 556 AGRWATTESIMADLAEIVRARRADA 580 AGRW T ++ ADL + VR R +A Sbjct: 540 AGRWPTAAAVFADLMD-VRRRHIEA 563 Lambda K H 0.317 0.135 0.396 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: 845 Number of extensions: 43 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: 583 Length of database: 573 Length adjustment: 36 Effective length of query: 547 Effective length of database: 537 Effective search space: 293739 Effective search space used: 293739 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 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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