Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-13349 (490 letters) >NCBI__GCF_000746085.1:WP_036262823.1 Length = 506 Score = 358 bits (918), Expect = e-103 Identities = 199/494 (40%), Positives = 284/494 (57%), Gaps = 17/494 (3%) Query: 4 YRNYINGEWVESAR--RFDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTTV 61 Y N+I G+WV + + F++++P+DG V+ V + E V+ A+ A HAA RGAWGRT+ Sbjct: 19 YDNFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAA-RGAWGRTSP 77 Query: 62 AERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAPL 121 AER+ L RIAD I+++ D E D GKP+ D+P +FR FA L+ Sbjct: 78 AERSLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEG 137 Query: 122 DTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEET 181 + D A Y +PLGVV I PWN PLL+ WK+APALA GN V+ KP+E+T Sbjct: 138 GISEIDHDTVA----YHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQT 193 Query: 182 PGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMRA 241 P + +L +++ + +PPGV N+++GFG + AG+ + N I + FTGE+ TG IM+ Sbjct: 194 PMSVMVLVDMIGDL-LPPGVLNVINGFGVE-AGKPLAQNKRIAKVAFTGETTTGRLIMQY 251 Query: 242 AATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVYVE 295 A+ ++ PV+ ELGGK+ I FAD F+K ++G L+ G+VC C R V+ Sbjct: 252 ASENIIPVTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFA-LNQGEVCTCPSRALVQ 310 Query: 296 RPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVGG 355 IY+RF++ V RVK +K G P D T +G S + +K+LSY + R+EGA+VL GG Sbjct: 311 EKIYDRFMERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGG 370 Query: 356 GVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKYG 415 G G GF+V+PTI+ G R +EE+FGP+ V+ F + EA+ +ANDT YG Sbjct: 371 GRADVGPELAGGFYVQPTILEG-HNKMRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYG 429 Query: 416 LSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFYS 475 L A WT N R +R A+ G W N + L FGG SGIGRE L+ Y Sbjct: 430 LGAGVWTRNGTRAYRFGRAIEAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQ 489 Query: 476 ELTNVCVRIDQEAV 489 + N+ V +A+ Sbjct: 490 KTKNMLVSYSPKAL 503 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: 592 Number of extensions: 33 Number of successful extensions: 8 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