Align alcohol dehydrogenase (EC 1.1.1.1); acetaldehyde dehydrogenase (acetylating) (EC 1.2.1.10) (characterized)
to candidate WP_027698995.1 TT13_RS05060 bifunctional acetaldehyde-CoA/alcohol dehydrogenase
Query= BRENDA::C7IV28 (872 letters) >NCBI__GCF_000691805.2:WP_027698995.1 Length = 900 Score = 721 bits (1862), Expect = 0.0 Identities = 398/897 (44%), Positives = 558/897 (62%), Gaps = 37/897 (4%) Query: 7 EKKETKEKTEVKETTDVKKQIDLLVERAKRAQEKFMSYTQEQINEIVKAMALAGIEKHVE 66 +KK + + K+ LV++A+ A ++F +Y+Q Q+++IV AMALAG E + Sbjct: 8 KKKVLTAEEKAARFEAAKEMTSALVDKAEIALKEFSTYSQAQVDKIVAAMALAGSENSLL 67 Query: 67 LAKLAHEETKMGVYEDKITKNLFAVEYVYNYIKDKKTVGILKENLEENYMEVAEPVGVIA 126 LA A+ ET GV EDK TKN FA E VYN IK KTVG++ E+ +E+A P+G++A Sbjct: 68 LAHEAYAETGRGVVEDKDTKNRFASESVYNAIKKDKTVGVINEDRVTGKVELAAPLGILA 127 Query: 127 GVTPVTNPTSTTMFKCLIAIKTRNPIIFSFHPKALKCSIEAAKTMYEAALKAGAPEGCIG 186 G+ P TNPTST +FK ++ KTRN I+F+FHP+A K S AAK +YEAA+ AGAP+ I Sbjct: 128 GIVPTTNPTSTAIFKSMLTAKTRNVIVFAFHPQAQKSSSHAAKIVYEAAVAAGAPKNFIQ 187 Query: 187 WIETPSIEATQLLMTHPDISLILATGGAGMVKAAYSSGKPALGVGPGNVPCYIEKTANIK 246 WIETPS++ T L+ +P I+ ILATGG MV AA SG P++GVG GN YI+KTANI Sbjct: 188 WIETPSLDGTSALIQNPKIASILATGGPSMVNAALRSGNPSMGVGAGNGAVYIDKTANIN 247 Query: 247 RAVSDLILSKTFDNGTVCASEQAVIIDEEIADEVKKLMREYGCYFLNKEETKKLEEFAID 306 RAV DL+LSK FDNG +CA+E +V+ID + DE ++ G Y K + K+ F Sbjct: 248 RAVEDLLLSKRFDNGMICATENSVVIDASVYDEFMAKLQAQGAYLTPKRDYDKIANFVFK 307 Query: 307 KNT---GLMNPAVVGQPATKIAQMAGFKVPENTKILVAEYPAVGPEYPLSREKLSPILAL 363 N G+ P V G IA+ AG K+P + +L+ E LS EKLSP+L++ Sbjct: 308 PNAEGFGVAGP-VAGMSGQWIAKNAGVKIPADKDVLLFELDKKNIGEALSSEKLSPLLSV 366 Query: 364 YTVKDYKEGIKRCEEMIQFGGLGHSAVIH--SENQQIINEFANRVQASRILVNAPASQGA 421 Y D +EGI+ + ++ + G GH+A I +++ + E+A+ + +RILVN P S G Sbjct: 367 YKAADRQEGIEIVQSLLNYQGAGHNAAIQIGAQDDPFVKEYADAIGVARILVNQPDSIGG 426 Query: 422 IGDIYNTAI-PSLTLGCGTMGGNSTTDNVSIYNLINIKRVFIRKERMKWFRVPPQIYFER 480 +GDIY A+ PSLTLG G+ G NS + N+S Y+L+NIK V R+ R +W R+P IY+E Sbjct: 427 VGDIYTDALRPSLTLGTGSWGKNSLSHNLSTYDLLNIKTVARRRNRPQWVRIPNNIYYES 486 Query: 481 GSLQYLSQVKS-KKAFIVTDPAMVKLGFIDKV--TYQLDKANIKHEIFSEVEPDPSVDTV 537 ++ YL ++ +AFIV DP MVK GF+DKV + L + IK ++ V+PDP++ Sbjct: 487 NAITYLQELPGVDRAFIVADPGMVKFGFVDKVLDQFALHETVIKTSLYGTVQPDPTLKQA 546 Query: 538 EKGVKIMKEFQPDLIIAVGGGSPIDAAKGMWLFYEYPDTK---------------FEDLR 582 + M +FQPD +I +GGGS +DA K YEY F+ + Sbjct: 547 IDIARQMAQFQPDTVITIGGGSALDAGKVGRFIYEYAQQPGHEGILDDDRALKELFQQMA 606 Query: 583 LKFMDIRKRTYKFPELGKKALFIAVPTTSGTGSEVTAFAVITDKKRNIKYPLADYELTPD 642 KFMDIRKR KF L +A+PTTSGTGSEVT FAVITD + ++KYPLADYELTP Sbjct: 607 QKFMDIRKRIVKFDHQVLTQL-VAIPTTSGTGSEVTPFAVITDDETHVKYPLADYELTPQ 665 Query: 643 IAIIDPDLTMTIPPSVTADTGMDALTHAIEAYVSVMASDYTDALAEKAIKLIFEYLPKAY 702 +AI+DP+ MT+P A +G+DAL+HA+E+YVSVM+S +T A +AIK IF+ L +Y Sbjct: 666 VAIVDPEFVMTVPKRTVAFSGLDALSHALESYVSVMSSQFTRPWALQAIKCIFDNLETSY 725 Query: 703 --------KNGQDKVAREKMHNASCIAGMAFTNAFLGINHSMAHILGAKFHLPHGRANAI 754 K GQ +AR K+H A+ +AGM+F NAFLG+NHS+AH +G +F LPHG A I Sbjct: 726 HYDPAHPTKEGQ--IARAKVHYAATLAGMSFANAFLGLNHSLAHKIGGEFGLPHGLAITI 783 Query: 755 LLPYVIEYNAELPK-KFAAFPQYEYPKAAEKYAEIAKMLGLPASTVEEGVKSLIEAIKNL 813 + +VI++NA K FP+YE A + YA+IA+ +GL V +L++ IK+L Sbjct: 784 AMSHVIKFNAVTGNVKRTPFPRYETYTAQKDYADIARHIGLEGKDDAALVDALLKKIKDL 843 Query: 814 MKELNLPLTLKEAGINKEEFEKQIMEMSDIAFNDQCTGSNPRMPLVSEIAEIYRKAY 870 L++ TL G+ K+ I +++D+ ++DQCT NPR P +SEI E+ Y Sbjct: 844 AAALDVNTTLSGNGVTKDALTNSIDKLTDLVYDDQCTPGNPRQPRLSEIKELLNDLY 900 Lambda K H 0.316 0.133 0.378 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: 1800 Number of extensions: 77 Number of successful extensions: 10 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: 872 Length of database: 900 Length adjustment: 43 Effective length of query: 829 Effective length of database: 857 Effective search space: 710453 Effective search space used: 710453 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 (21.6 bits) S2: 56 (26.2 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