Align acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_073041910.1 BUB04_RS17530 aldehyde dehydrogenase EutE
Query= metacyc::MONOMER-20853 (484 letters) >NCBI__GCF_900129305.1:WP_073041910.1 Length = 476 Score = 635 bits (1639), Expect = 0.0 Identities = 326/484 (67%), Positives = 389/484 (80%), Gaps = 8/484 (1%) Query: 1 MDVRQQDVERIVVEVLKKMMSDQPTAAATTVVAASGCDCGDFGLFDRLEDAVQAAEAAQK 60 M +RQ+D+E IV +VL ++ + P A A G D+G+F+RLEDAV+AA A Sbjct: 1 MALRQEDIENIVQQVLLQLTHEAPAAPTQRPGGAQG----DWGVFERLEDAVEAAREAYP 56 Query: 61 KISTVAMRDKIIAAIRKAGLENAKAFAEIAHNETGMGRVSDKIAKNILVCERTPGTECLS 120 +I TVAMR++++ IR+A NA+ AE+A ETGMGRV DK+ KN+LV ERTPG E L Sbjct: 57 RIGTVAMRERVVTVIRRAARANARRLAEMAVEETGMGRVEDKVKKNLLVAERTPGPEILH 116 Query: 121 PMAISGDMGLTLIENAPWGVIASVTPSTNPTATVINNAISMIAGGNSVIFAPHPNAKRAS 180 P AI+GD GLTLIENAPWGVIASVTPSTNP ATVINNAISM++GGN+V+FAPHP AKR S Sbjct: 117 PSAITGDAGLTLIENAPWGVIASVTPSTNPAATVINNAISMLSGGNAVVFAPHPGAKRVS 176 Query: 181 QTAIQVLNKAIIEATGVANLLVAVKEPTIEVAQELFSHPRIKLLVVTGGEAVVAQARKVA 240 Q I++LN+AI E TG+ NLL V+EP+I+VAQ+LF+ P I LLVVTGGEAVV ARK Sbjct: 177 QETIRMLNQAIHEETGIDNLLTCVREPSIQVAQQLFTFPGIHLLVVTGGEAVVEAARKAT 236 Query: 241 TMRLIAAGAGNPPVVVDETANIARAARSIYDGASFDNNIICADEKEIIAVDSIADQLKAE 300 RLIAAGAGNPPVVVDETA++ARAA+SIYDGASFDNNIIC DEKEIIAV+SIAD LKAE Sbjct: 237 NKRLIAAGAGNPPVVVDETADLARAAQSIYDGASFDNNIICCDEKEIIAVESIADALKAE 296 Query: 301 MKAIGAVEISLEQADAVARVVLRNYPQVEGGKAPNPNPKWVGRDAALIAKAAGIDVPDSC 360 +K GAVEI+ +QA+AVAR VL +YP G PNP+WVGRDA +A+A G VP Sbjct: 297 LKRCGAVEITPQQAEAVARAVLLDYP----GPNARPNPQWVGRDAHKLAEAGGFAVPPET 352 Query: 361 RLLIVDVKRDINHVFARVEQLMPVIPLLRAANVDEAIEWALILERGLSHTAGMHSRNIDN 420 RLL VDV RD++HVFARVEQ+MP++PLLRA + +EA+EWA+ILERGLSHTAG+HSRNID+ Sbjct: 353 RLLFVDVGRDLDHVFARVEQMMPLLPLLRAKDFEEALEWAIILERGLSHTAGLHSRNIDH 412 Query: 421 MDKMARAMNTSLFVKNGPHLAALGAGGEGWTTMTISTPTGEGVTCARSFVRLRRCCVVDN 480 MD MA +NTSLFVKNGPHLA LGAGGEGWT+MTISTPTGEGVT AR+FVRLRRC +V + Sbjct: 413 MDIMATRVNTSLFVKNGPHLAGLGAGGEGWTSMTISTPTGEGVTNARTFVRLRRCTLVGS 472 Query: 481 FRIV 484 FRIV Sbjct: 473 FRIV 476 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: 712 Number of extensions: 33 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: 484 Length of database: 476 Length adjustment: 34 Effective length of query: 450 Effective length of database: 442 Effective search space: 198900 Effective search space used: 198900 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