Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_011425015.1 RHE_RS08800 aldehyde dehydrogenase family protein
Query= SwissProt::Q9H2A2 (487 letters) >NCBI__GCF_000092045.1:WP_011425015.1 Length = 506 Score = 319 bits (818), Expect = 1e-91 Identities = 186/477 (38%), Positives = 275/477 (57%), Gaps = 14/477 (2%) Query: 14 IDGKFLPCSSY-IDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPS--WSSRSPQERS 70 IDGK+ +S+ I+ PS G R P + E A+ AAR+AF W + ERS Sbjct: 22 IDGKWEAGASHPIERIAPSHGVTVSRFPAGSATDAERAIAAARKAFDEGPWPRMTASERS 81 Query: 71 RVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSS--LHHTSEC 128 +L + ADL+ EE A ++ + GK + R +I SV +R+ A+ + LH S Sbjct: 82 AILLKAADLIAARAEELAFLDAIEAGKPITQVRG-EIAGSVDIWRYAAALARDLHGESYN 140 Query: 129 TQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAW 188 T D G + +R +GV +I+PWN P ++ K+ A+AAG T + KPSELTS + Sbjct: 141 TLGD--GTVGVVLREAIGVVSIITPWNFPFLIVGQKLPFALAAGCTTVVKPSELTSGSTL 198 Query: 189 MLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCK 248 +L ++L +AGVP GVVNIV GTGP VG + SHP+V +ISFTGS + + +A K Sbjct: 199 VLGEILQQAGVPDGVVNIVTGTGPEVGAVMTSHPDVDMISFTGSTGVGKLTMKNAAQTLK 258 Query: 249 KLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFV 308 K+SLELGGKNP I+F DA+LD I A V ++ N GE C SR+ + KSI S+ ++R Sbjct: 259 KVSLELGGKNPQIVFPDADLDAFIDAAVFGAYFNAGECCNAGSRLILHKSIASDVVRRVA 318 Query: 309 EATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQ 368 E ++ KVG P DP +GA+I+ HLEK+ YV A + GA++ G L + Sbjct: 319 ELSKGVKVGDPLDPQTQVGAIITPQHLEKISGYVAGARSNGARVTHGGETLDLGM----- 373 Query: 369 AGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNV 428 G FM PT++ + + EE+FGPV V+ F++ E + AN++ YGL+A VWS + Sbjct: 374 -GQFMSPTILEAVTPDMAVAREEVFGPVLSVLTFETTAEAVRIANSIDYGLSAGVWSRDF 432 Query: 429 GRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITV 485 + + +++G +W N ++ LPFGG K SG+GRE + + + +TE KT+ + Sbjct: 433 DTCLTIGRSVRAGTIWMNTFMDGASELPFGGYKQSGLGRELGRHAVEDYTETKTLNM 489 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: 554 Number of extensions: 18 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: 506 Length adjustment: 34 Effective length of query: 453 Effective length of database: 472 Effective search space: 213816 Effective search space used: 213816 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