Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_019615884.1 G327_RS0116375 bifunctional acetaldehyde-CoA/alcohol dehydrogenase
Query= CharProtDB::CH_024820 (891 letters) >NCBI__GCF_000381745.1:WP_019615884.1 Length = 879 Score = 1227 bits (3174), Expect = 0.0 Identities = 607/883 (68%), Positives = 728/883 (82%), Gaps = 4/883 (0%) Query: 1 MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60 M V+ VA+L AL+ RVK AQ EYA+F+QE+VD+IFR AAL + RI LAKMAV E+GMG Sbjct: 1 MTVSTVADLEALIARVKLAQAEYATFSQEKVDEIFRVAALKVSTHRIELAKMAVKETGMG 60 Query: 61 IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120 I+EDKVIKNHFASE+IYN++ D KT G LS +++ T+T+AEP+GIIC IVPTTNPTSTA Sbjct: 61 IIEDKVIKNHFASEFIYNSFADTKTVGELSRNESLNTVTLAEPMGIICAIVPTTNPTSTA 120 Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180 IFK+L++LKT N I +PHPRAK+ TN AA IVL AAI AGAPKD+IGWID PS+EL+N Sbjct: 121 IFKTLMALKTGNGCIVAPHPRAKECTNYAAKIVLDAAIEAGAPKDIIGWIDIPSLELTNT 180 Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240 +M H D +ILATGGPGMVKAAYSSG PAIGVGAGNTPVVIDE+ADIKRAV+S+LMSKTF Sbjct: 181 IMKHDDTAIILATGGPGMVKAAYSSGNPAIGVGAGNTPVVIDESADIKRAVSSILMSKTF 240 Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300 DNG+ICASEQ+ +VV+S YD + R +GG++L + K V D + +GALNA IVGQ Sbjct: 241 DNGMICASEQAAIVVESKYDEFKARLEEYGGFMLNEADTKKVADTMFIDGALNAKIVGQS 300 Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360 A+ IAELAG VP +TK+L+GE V E FAHEKLSPTL +++AK++EDAV +A+ ++ Sbjct: 301 AFTIAELAGVKVPTSTKVLVGEGLEVKEENMFAHEKLSPTLGLFKAKNYEDAVRQAQIVL 360 Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420 +GG+GHT+ LYTDQD RV FG MK RI+IN+P S GGIGD+YNF APSLTLG Sbjct: 361 DIGGVGHTAALYTDQDANSERVDAFGLAMKACRIVINSPTSHGGIGDIYNFGFAPSLTLG 420 Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480 CG+ GN++SENVGP+HLIN KT+AKRAENMLWHKLPKSIYFRRGSLPIA+ ++ +G + Sbjct: 421 CGTHSGNAVSENVGPQHLINTKTIAKRAENMLWHKLPKSIYFRRGSLPIAMTDL--EGKQ 478 Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540 RA+IVTD FLF NGY D++ S+L++ G+ EVF EVEADPTLSI++KGA N+F PDVI Sbjct: 479 RAMIVTDGFLFANGYIDELRSILESKGMMVEVFHEVEADPTLSIIQKGAAACNAFNPDVI 538 Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600 +A+GGGSPMDAAKIMWV+YEHP T FE+LA+RFMDIRKRIYKFPKMGVKA+++ +TTTSG Sbjct: 539 LAVGGGSPMDAAKIMWVLYEHPATDFEDLAMRFMDIRKRIYKFPKMGVKAELVCITTTSG 598 Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660 TGSEVTPFAVVTDD TG+KYPLADY LTP+MA+VDANLVMDMPKSLCAFGG DAVTHA+E Sbjct: 599 TGSEVTPFAVVTDDKTGKKYPLADYELTPNMAVVDANLVMDMPKSLCAFGGYDAVTHAVE 658 Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720 AYVS+LA+E+SDGQALQ+LKLLKEYLP+SYH G + VARE+VH+AATIAGIAFAN+FLG Sbjct: 659 AYVSMLANEYSDGQALQSLKLLKEYLPSSYHNGKNDAVAREKVHNAATIAGIAFANSFLG 718 Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780 VCHSMAHK+G++FHIPHGLANALL+ N IR+NA + PTKQ FSQYDRP+AR RYAEIA Sbjct: 719 VCHSMAHKIGNEFHIPHGLANALLLTNTIRFNATNKPTKQGTFSQYDRPKARARYAEIAV 778 Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840 HLG T KI LL WL+ LK EL IP SI+ AGV EADFLA +D L+E AFDDQ Sbjct: 779 HLGFYE--GNTEDKINALLTWLDELKVELNIPLSIQAAGVNEADFLAALDDLAEQAFDDQ 836 Query: 841 CTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKA 883 CTGANPRYPLISELK++LL +YYG+DYV+ A E +A Sbjct: 837 CTGANPRYPLISELKEVLLASYYGKDYVDVVDAPAVEETEEEA 879 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: 1852 Number of extensions: 69 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: 879 Length adjustment: 43 Effective length of query: 848 Effective length of database: 836 Effective search space: 708928 Effective search space used: 708928 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