Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_046008433.1 OLEAN_RS05730 aldehyde dehydrogenase EutE
Query= metacyc::MONOMER-20853 (484 letters) >NCBI__GCF_000967895.1:WP_046008433.1 Length = 468 Score = 531 bits (1369), Expect = e-155 Identities = 283/479 (59%), Positives = 355/479 (74%), Gaps = 19/479 (3%) Query: 6 QDVERIVVEVLKKMMSDQPTAAATTVVAASGCDCGDFGLFDRLEDAVQAAEAAQKKISTV 65 Q +E IV V++++ + Q D +G++ L+DAV AA+ AQ +I ++ Sbjct: 9 QQLEMIVKRVIEQLHAPQK-------------DGERYGVYQTLDDAVAAAKIAQPQIRSL 55 Query: 66 AMRDKIIAAIRKAGLENAKAFAEIAHNETGMGRVSDKIAKNILVCERTPGTECLSPMAIS 125 A R+ IIA+IRK E+ + +E+A ETG GRVSDKI KN LV +RTPGTE L PMAI+ Sbjct: 56 AKRNAIIASIRKLASEHIQELSELAVQETGFGRVSDKIRKNRLVIDRTPGTEVLIPMAIT 115 Query: 126 GDMGLTLIENAPWGVIASVTPSTNPTATVINNAISMIAGGNSVIFAPHPNAKRASQTAIQ 185 GD GL+L+ENAPWGVIASVTPSTNP+AT+INN+ISMIA GN+V+F+PHP AK SQ IQ Sbjct: 116 GDHGLSLVENAPWGVIASVTPSTNPSATIINNSISMIAAGNAVVFSPHPAAKAVSQRTIQ 175 Query: 186 VLNKAIIEATGVANLLVAVKEPTIEVAQELFSHPRIKLLVVTGGEAVVAQARKVATMRLI 245 ++N+A ++A G ++ ++ PT+E A +LFS+P I LL VTGG+AVV+ ARKV RLI Sbjct: 176 LVNQASVKAGGPNGIVTCLEVPTLEAATQLFSYPGIHLLTVTGGDAVVSAARKVTDKRLI 235 Query: 246 AAGAGNPPVVVDETANIARAARSIYDGASFDNNIICADEKEIIAVDSIADQLKAEMKAIG 305 AAG GNPPVVVDETA+I RAA SI GASFDNNI+C DEKEIIAV+SIAD LKA M G Sbjct: 236 AAGPGNPPVVVDETADIERAAISIVQGASFDNNIVCVDEKEIIAVESIADALKAAMVRNG 295 Query: 306 AVEISLEQADAVARVVLRNYPQVEGGKAPNPNPKWVGRDAALIAKAAGIDVPDSCRLLIV 365 AVEIS +QA+AVA++VL +YP G P +WVGRDAA IA AAG +VP S RLL++ Sbjct: 296 AVEISAQQAEAVAQLVLHDYP----GPKAAPKSEWVGRDAAKIAAAAGFEVPASTRLLLL 351 Query: 366 DVKRDINHVFARVEQLMPVIPLLRAANVDEAIEWALILERGLSHTAGMHSRNIDNMDKMA 425 + D +HVFAR E +MPVI + RA + D+AI+WA+ LE H+A MHSRNIDN+ +MA Sbjct: 352 EA--DYDHVFARTEMMMPVIAMSRARDCDQAIDWAIELENDNKHSAAMHSRNIDNLSRMA 409 Query: 426 RAMNTSLFVKNGPHLAALGAGGEGWTTMTISTPTGEGVTCARSFVRLRRCCVVDNFRIV 484 +NTSLFVKNGP +A LGAGGEGW +MTISTPTGEGVT A +FVR RRC +VD FRIV Sbjct: 410 EEINTSLFVKNGPCIAGLGAGGEGWASMTISTPTGEGVTNAATFVRKRRCTLVDAFRIV 468 Lambda K H 0.318 0.132 0.375 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: 597 Number of extensions: 20 Number of successful extensions: 3 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: 484 Length of database: 468 Length adjustment: 33 Effective length of query: 451 Effective length of database: 435 Effective search space: 196185 Effective search space used: 196185 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. 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