Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-13361 (500 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 221 bits (562), Expect = 6e-62 Identities = 140/469 (29%), Positives = 244/469 (52%), Gaps = 27/469 (5%) Query: 38 INPVNGKLISDVFEADA----KQVNEAVVAAQNALKGPWGKLSVQDRAALIHKIADGIQA 93 +NP NG++ S+ +A K +N A++A++ A K ++ R + + +A + Sbjct: 21 VNPYNGEVASEFVTCNADDAKKALNIALLASKEA-----SKTTIAQRCSWLLDVASKLAQ 75 Query: 94 RFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMST-SDGSGALN 152 E+ + G+P+ +R +++ R I A+ +T H + + G ++ Sbjct: 76 NKEDIAKTITDEVGKPITYSR-IEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTIS 134 Query: 153 YTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAG 212 + R P GV+ I+P+N PL L K+APAL GN V+ KP+ E+P +A A++ ++ Sbjct: 135 FFSRVPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESE 194 Query: 213 VP-PGVFNLIHGFGKDSAGEFLTQH-PGISALTFTGESKTGSTIMKAVADGVKEVSFELG 270 ++++G D G +T P + ++FTG G I K+ G+K+VS ELG Sbjct: 195 FAIKDALSVVYG-DADVGGTLVTSEIPRV--ISFTGSVGVGEIITKSA--GIKKVSLELG 249 Query: 271 GKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLV 330 G A + A+LD A + +F NSGQVC+ +R+YVH+ I+ EF + ++LV Sbjct: 250 GNAATFIDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLV 309 Query: 331 VGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERDQGAYVQPTI 390 VG P ++ MGPL++ + + + + A+ EGAT + + R +G P + Sbjct: 310 VGSPYEEDTFMGPLVNDEAAKRAMEWVQSAIKEGATPIL--------EPRVEGRVFYPCV 361 Query: 391 WTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQ 450 + + V +E+F P+ + D DE + +N+S YGL +I+T +L+ R + Sbjct: 362 MADVKEDMAIVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINE 421 Query: 451 IHVGLVWVNTW-YLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICI 498 + G + +N LR P+GGVKLSG+GREG RF+++ S+I ++ I Sbjct: 422 LDAGGIVINDMPTLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470 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: 483 Number of extensions: 17 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: 471 Length adjustment: 34 Effective length of query: 466 Effective length of database: 437 Effective search space: 203642 Effective search space used: 203642 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