Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_086510113.1 BZY95_RS11785 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-13349 (490 letters) >NCBI__GCF_002151265.1:WP_086510113.1 Length = 506 Score = 345 bits (886), Expect = 2e-99 Identities = 194/494 (39%), Positives = 283/494 (57%), Gaps = 21/494 (4%) Query: 2 KQYRNYINGEWVESARR--FDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRT 59 ++Y NYI GE+V + FD+V+PV+G V Q+ + E +D A+ A HAA AWGRT Sbjct: 17 QRYGNYIGGEFVPPVKGQYFDNVSPVNGEVFCQIPRSTAEDIDKALDAAHAAAP-AWGRT 75 Query: 60 TVAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTA 119 + ER+ IL ++AD I++ + AE D GK V D+P +FR FA ++ Sbjct: 76 SATERSNILLKMADRIEQNLEKLAVAETWDNGKAVRETLNADLPLAIDHFRYFAGCIRAQ 135 Query: 120 PLDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSE 179 D A ++Y +PLGVVG I PWN PLL+ WK+APALA GN VV KP+E Sbjct: 136 EGTAADID----ANTVSYHFHEPLGVVGQIIPWNFPLLMAVWKLAPALAAGNCVVLKPAE 191 Query: 180 ETPGTATLLAEVMHTVG--VPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSA 237 +TP + + E+M VG +PPGV N+V+G+G + AG+ + T+ I I FTG + G+ Sbjct: 192 QTPAS---VLELMKLVGDLLPPGVVNVVNGYGAE-AGQALATSKRIAKIAFTGSTPVGAH 247 Query: 238 IMRAAATHVKPVSFELGGKNAAIIFAD------CDFEKMIDGMMRAVFLHSGQVCLCAER 291 I++ AA ++ P + ELGGK+ I FAD EK +G++ A F + G+VC C R Sbjct: 248 ILKCAADNIIPSTVELGGKSPNIYFADIMDAEPAFIEKAAEGLVLA-FFNQGEVCTCPSR 306 Query: 292 VYVERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQV 351 ++ IY+ F+ +ERV +K G P D +G S E DK++SY +AREEGA+ Sbjct: 307 ALIQEDIYDAFMAKVMERVGKIKRGNPLDTDVQVGAQASQEQFDKIMSYMDIAREEGAEF 366 Query: 352 LVGGGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALAND 411 L GG F A D G++++PT++ G R +EE+FGP+ V+ F EAEA+A+AND Sbjct: 367 LTGGDKESFDPAYDKGYYIQPTLLKG-NNKMRVFQEEIFGPVVAVTTFKDEAEALAIAND 425 Query: 412 TKYGLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSL 471 T++GL A W+ ++N R+ ++ G W N + FGG SG+GRE +L Sbjct: 426 TEFGLGAGVWSRDINVAFRMGRGIQAGRVWTNCYHQYPAHAAFGGYKKSGVGRETHKVAL 485 Query: 472 NFYSELTNVCVRID 485 Y + N+ V D Sbjct: 486 EHYQQTKNLLVSYD 499 Lambda K H 0.321 0.137 0.420 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: 601 Number of extensions: 24 Number of successful extensions: 7 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: 490 Length of database: 506 Length adjustment: 34 Effective length of query: 456 Effective length of database: 472 Effective search space: 215232 Effective search space used: 215232 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 (21.8 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