Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 225 bits (574), Expect = 2e-63 Identities = 147/440 (33%), Positives = 225/440 (51%), Gaps = 20/440 (4%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERI 74 IDG+F+ S D +NPAT++ L V +E+D AV AAK+A W+K R Sbjct: 12 IDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFK-TWRKTPIGTRA 70 Query: 75 AVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQ 134 + K LI E EL+ S + GK T D+ R ++ I N Q Sbjct: 71 RIFLKYQQLIRENMSELAHTLSAEQGK-TVPDAEGDVFRGLE----VVEHAAAIGN--LQ 123 Query: 135 MDDVALN-------YAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTP 187 + ++A N Y + +P+GV I P+N P ++ W A+A GNT V+KP+E P Sbjct: 124 LGELANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDP 183 Query: 188 MTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASA 247 M L E+ +AG+P GV+N+VH G A+ +HPD+ A+SF G T G + A Sbjct: 184 MVTMRLVELALEAGIPKGVLNVVH--GGEEVVNAICDHPDIKAVSFVGSTRVGTHVYNRA 241 Query: 248 AKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAF 307 + KR+ +G KN V+ D+N ++ + + ++F G+ C+ S + + A ++ Sbjct: 242 SLAGKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEA-RSW 300 Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRP--EG 365 + VAK K L V A T VG +IS ERV G I +E+G T+ G+ P +G Sbjct: 301 VPDLVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDG 360 Query: 366 LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTN 425 EKG F+ PTI +G+T D R+ +EEIFGPV+ ++ +T E+ + +N G +V+T Sbjct: 361 FEKGNFVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQ 420 Query: 426 DLRRAHRVAGQIEAGIVWVN 445 A + I+ G V +N Sbjct: 421 SGAAARKFQEDIDVGQVGIN 440 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: 545 Number of extensions: 30 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: 486 Length of database: 501 Length adjustment: 34 Effective length of query: 452 Effective length of database: 467 Effective search space: 211084 Effective search space used: 211084 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 Apr 09 2024. 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