Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_001906585.1:WP_073950325.1 Length = 511 Score = 365 bits (938), Expect = e-105 Identities = 190/475 (40%), Positives = 284/475 (59%), Gaps = 5/475 (1%) Query: 10 DCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMT 69 D +I G+ G+T ++PAT E++ T G ++D AV AA++A G W T Sbjct: 20 DGAQYIAGRLTKGTSGRTHAVVDPATGEEVHTYELAGPDDVDAAVAAAREAFPG-WAGAT 78 Query: 70 ANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTIT 129 +R L + +++ +R E+ + ESL GKP L+ D+P N FF+ R + Sbjct: 79 PGDRSDALHRFAEVLADRAEDFARAESLQCGKPLKLTREFDVPGTIDNAAFFAGAARHLQ 138 Query: 130 NE-ATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPM 188 + A + +Y R P+GV+G I PWN PL + WK+ PA+AAGNT+V+KPAELTP+ Sbjct: 139 GQSAGEYSGDHTSYVRREPIGVVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPL 198 Query: 189 TATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAA 248 T+ + A+ +AG+PDGV+N+V G G AG L HPDV +SFTG T GK + A Sbjct: 199 TSLLFAQAATEAGIPDGVINIVTGTG-KEAGEHLVGHPDVAMVSFTGSTAVGKRVAEIAT 257 Query: 249 KTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFL 308 ++KRL ELGGK P V+F D++L+ + + + IN G+ C +R YV+RP YE F+ Sbjct: 258 ASVKRLHLELGGKAPFVVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLYEEFV 317 Query: 309 EKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEG-LE 367 + A + + +GDPF T +G LIS H +RV G++ A ++TGG+ P+G L+ Sbjct: 318 ARTAALMETVRLGDPFAPGTDLGPLISHVHRDRVAGFVDRA-RAYARVVTGGEAPQGELK 376 Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427 G + PT+I G +D +V+ EIFGPV+ V+PFD+++E + NDT YGL+AS W+ D+ Sbjct: 377 NGAYYRPTLIAGAAQDSEIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDV 436 Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482 RA+R +I+AG VWVN P GG KQSG G++ +SFE Y+++ ++ Sbjct: 437 YRANRATREIKAGCVWVNDHIPIISEMPHGGSKQSGFGKDMSSYSFEEYTQIKHV 491 Lambda K H 0.318 0.136 0.404 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: 605 Number of extensions: 19 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: 486 Length of database: 511 Length adjustment: 34 Effective length of query: 452 Effective length of database: 477 Effective search space: 215604 Effective search space used: 215604 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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