Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_041097806.1 SUTH_RS05840 aldehyde dehydrogenase family protein
Query= SwissProt::Q9H2A2 (487 letters) >NCBI__GCF_000828635.1:WP_041097806.1 Length = 479 Score = 285 bits (730), Expect = 2e-81 Identities = 164/474 (34%), Positives = 265/474 (55%), Gaps = 13/474 (2%) Query: 13 FIDGKFLPCSSY--IDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERS 70 +IDG+++ + I+ + P+ G + VP + + AV AAR AF +WS ER+ Sbjct: 8 YIDGQWVSPAGQGTIEVFSPTDGALLATVPQGNAADADKAVTAARGAFDAWSVTPAAERA 67 Query: 71 RVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECTQ 130 L ++ + L+ +E A+ + + G ++ + + +F ++ E Sbjct: 68 AYLKKIQESLKARADEIAKTITLEMGMPYKFSQRIQVGSPTASFGMYSKMLADFPFE--- 124 Query: 131 MDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWML 190 + +G VR VGV I+PWN PL+ + K+A A+AAG TV+ KPSE+ + A++L Sbjct: 125 -EKVGNSK-VVREAVGVVAAITPWNYPLHQIAAKVAAALAAGCTVVLKPSEVAPLNAFLL 182 Query: 191 CKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKL 250 +++ AGVP GV N++ G GP VGEA+V+H EV ++SFTGS R+++L++ K++ Sbjct: 183 AEIIHAAGVPAGVFNLITGYGPVVGEAMVTHREVDMVSFTGSTRAGTRVSELASATVKRV 242 Query: 251 SLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVEA 310 +LELGGK+ AII +DA+ + + V + + N G+ C +R+ V + Y+E K VEA Sbjct: 243 ALELGGKSAAIILDDADFNVAVKGVVGNCYLNSGQTCTAHTRMLVPATRYAEAAKLAVEA 302 Query: 311 TRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLP-ARNQA 369 + ++VG P V++G L SK ++VR Y+ + +AEG ++ G G D LP N Sbjct: 303 AQAYRVGDPMAEGVTLGPLASKMQQDRVRDYIGKGIAEGCELLTG-GAD---LPEGVNPD 358 Query: 370 GYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVG 429 GY++ PT+ +K +S EEIFGPV ++ + EE+ + AN YGLA VWS+ Sbjct: 359 GYYVKPTIFGKVKPDSSIAQEEIFGPVLSIISYADEEDAVSIANGTVYGLAGGVWSATDE 418 Query: 430 RVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTI 483 +VA+++++G V N + PFGG K SG GRE K + F E K + Sbjct: 419 HAEQVARRMRTGQVEINGGTF-NMYAPFGGYKQSGNGRELGKYGLEDFLEFKAM 471 Lambda K H 0.319 0.133 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: 504 Number of extensions: 19 Number of successful extensions: 4 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: 487 Length of database: 479 Length adjustment: 34 Effective length of query: 453 Effective length of database: 445 Effective search space: 201585 Effective search space used: 201585 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