Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_039105833.1 FPB0191_RS10160 bifunctional acetaldehyde-CoA/alcohol dehydrogenase
Query= CharProtDB::CH_024820 (891 letters) >NCBI__GCF_000807275.1:WP_039105833.1 Length = 890 Score = 1339 bits (3465), Expect = 0.0 Identities = 670/889 (75%), Positives = 762/889 (85%), Gaps = 5/889 (0%) Query: 1 MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60 MAVT++ EL+ L+ RVK+AQ+ YA+FTQEQVDKIF AAA AAA ARIPLA+ AVAESGMG Sbjct: 1 MAVTSLKELDELLVRVKQAQQVYATFTQEQVDKIFVAAATAAAAARIPLAQQAVAESGMG 60 Query: 61 IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120 IVEDKVIKN FA+EYI N Y+++KTCG+++E+D FGTITIAEP+GIICGIVPTTNPTSTA Sbjct: 61 IVEDKVIKNLFAAEYILNKYRNDKTCGIVAENDPFGTITIAEPLGIICGIVPTTNPTSTA 120 Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180 IFKSLISLKTRNAI+FSPHPRAK +T +AA IVL AAI AGAPKD+IGWID+PS+ELSNA Sbjct: 121 IFKSLISLKTRNAIVFSPHPRAKKSTIEAARIVLDAAIKAGAPKDIIGWIDEPSIELSNA 180 Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240 LMHH DI ILATGGPGMVKAAYSSGKPA+GVGAGNTPV+IDETAD+KRAVASVLMSKTF Sbjct: 181 LMHHDDIAAILATGGPGMVKAAYSSGKPALGVGAGNTPVIIDETADLKRAVASVLMSKTF 240 Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKN-GALNAAIVGQ 299 DNG+ICASEQ++VVVDSVYD VR +G Y+L KE KAVQ +IL + GALNA IVGQ Sbjct: 241 DNGMICASEQAIVVVDSVYDEVRRLLTHYGAYVLNAKETKAVQGIILNDKGALNANIVGQ 300 Query: 300 PAYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKL 359 PA KIAELAG VP +K+L+GEV+ VD SEPFAHEKLSPTLAM++AK FEDAV+KAEKL Sbjct: 301 PATKIAELAGIKVPAGSKVLVGEVSKVDLSEPFAHEKLSPTLAMFKAKSFEDAVDKAEKL 360 Query: 360 VAMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTL 419 V MGG+GHTS LYTDQD R++YFG KMKT RILIN PA+ GGIGDLYNF LAPSLTL Sbjct: 361 VEMGGLGHTSVLYTDQDRNRERITYFGSKMKTCRILINQPAAHGGIGDLYNFDLAPSLTL 420 Query: 420 GCGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGH 479 GCGSWGGNS+SENVGPKHLINKK +AKRAENMLWHKLP SIYF+RGSLP+AL EVI G Sbjct: 421 GCGSWGGNSVSENVGPKHLINKKVIAKRAENMLWHKLPSSIYFKRGSLPVALSEVIEQGA 480 Query: 480 KRALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDV 539 KR +VTD+FLFNNGY+ QIT L+A GV E FF+VEADPTLS+VRKG E ++FKPD Sbjct: 481 KRVFVVTDKFLFNNGYSKQITDQLEAQGVICETFFDVEADPTLSVVRKGTESMSAFKPDT 540 Query: 540 IIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTS 599 IIALGGGSPMDAAKIMWV+YEHPET F+ELALRFMDIRKR FP MG KAK+I VTTTS Sbjct: 541 IIALGGGSPMDAAKIMWVLYEHPETKFDELALRFMDIRKRTCHFPNMGEKAKLICVTTTS 600 Query: 600 GTGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAM 659 GTGSEVTPFAVVTDDATGQKYPLADYA+TP+MAIVDANLVM MPKSLCA GG DAVTHA+ Sbjct: 601 GTGSEVTPFAVVTDDATGQKYPLADYAITPNMAIVDANLVMTMPKSLCAAGGYDAVTHAL 660 Query: 660 EAYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFL 719 EAYVS++ASEFSDGQALQAL LLK YLPASY EG+ NP+ARE+VHSAAT+AG+AFA AFL Sbjct: 661 EAYVSIMASEFSDGQALQALSLLKAYLPASYKEGANNPIAREKVHSAATLAGVAFAQAFL 720 Query: 720 GVCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIA 779 GVCHSMAHK+G+ FHIPHG+ANA+LI NV+R+NA D PTKQ FSQY P+A RYAEIA Sbjct: 721 GVCHSMAHKIGAAFHIPHGVANAMLISNVVRFNATDKPTKQGTFSQYGHPKAVSRYAEIA 780 Query: 780 DHLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDD 839 DHLGL++ D+ K+EKL+ WL+ L+ +L IP SI+E G+ E FL+ VD+L+ DAFDD Sbjct: 781 DHLGLTSASDKDDKKVEKLIGWLDQLRKDLDIPFSIKEFGIDEKLFLSQVDQLAVDAFDD 840 Query: 840 QCTGANPRYPLISELKQILLDTYYGRDYVE----GETAAKKEAAPAKAE 884 QCTGANPRYPLI+ELKQILLDTYYGR Y + E A K AA A+ Sbjct: 841 QCTGANPRYPLIAELKQILLDTYYGRPYQDKGDISEDVAIKTAAKGAAK 889 Lambda K H 0.317 0.132 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: 1930 Number of extensions: 64 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: 891 Length of database: 890 Length adjustment: 43 Effective length of query: 848 Effective length of database: 847 Effective search space: 718256 Effective search space used: 718256 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 (21.7 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