Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-13361 (500 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 195 bits (496), Expect = 3e-54 Identities = 142/482 (29%), Positives = 236/482 (48%), Gaps = 22/482 (4%) Query: 24 IDGNFVTSASSFAN--INPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRA 81 IDG F+ S+++ +NP +++ V A +V++AV AA+ A K W K + RA Sbjct: 12 IDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFK-TWRKTPIGTRA 70 Query: 82 ALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFE 141 + K I+ E A+ G+ V A D+ R + A + L E Sbjct: 71 RIFLKYQQLIRENMSELAHTLSAEQGKTVPDAEG-DVFRGL---EVVEHAAAIGNLQLGE 126 Query: 142 MSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSA 201 ++ + +G YT+ +PLGV I+P+N P ++ W A+A GNT V KPSE+ P Sbjct: 127 LANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMVT 186 Query: 202 TLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADG 261 L E+ +AG+P GV N++H G + + HP I A++F G ++ G+ + + Sbjct: 187 MRLVELALEAGIPKGVLNVVH--GGEEVVNAICDHPDIKAVSFVGSTRVGTHVYNRASLA 244 Query: 262 VKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSG 321 K V +G KN AVV DA+ + + ++ ++F +GQ C+ + + + +V Sbjct: 245 GKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEA-RSWVPD 303 Query: 322 LKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERD 381 L +A+ L V G ++GP+IS R++V +++GAT+ G P+ D + Sbjct: 304 LVAKAKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQV-DGFE 362 Query: 382 QGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNL 441 +G +V PTI++G++ R EEIFGPV I + ++ I VN + G A++T + Sbjct: 363 KGNFVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQSG 422 Query: 442 SRAHRVSRQIHVGLVWVNTWYLRDLRTP-----FGGVKLSGLGREG--GRFSMDFYSDIA 494 + A + I VG V +N + P F G + S LG G G+ + FY+ Sbjct: 423 AAARKFQEDIDVGQVGINV----PIPVPVPLFSFTGSRASKLGDLGPYGKQVVMFYTQTK 478 Query: 495 NI 496 I Sbjct: 479 TI 480 Lambda K H 0.318 0.135 0.405 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: 502 Number of extensions: 24 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: 500 Length of database: 501 Length adjustment: 34 Effective length of query: 466 Effective length of database: 467 Effective search space: 217622 Effective search space used: 217622 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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