Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate WP_053936073.1 WG78_RS01880 bifunctional acetaldehyde-CoA/alcohol dehydrogenase
Query= CharProtDB::CH_024820 (891 letters) >NCBI__GCF_001294205.1:WP_053936073.1 Length = 888 Score = 1362 bits (3525), Expect = 0.0 Identities = 683/891 (76%), Positives = 774/891 (86%), Gaps = 4/891 (0%) Query: 1 MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60 MAVTNV EL+ALV RVKKAQ+++A+F+QEQVD+IFR AALAAADARIPLA+MAV E+GMG Sbjct: 1 MAVTNVQELDALVARVKKAQQQFATFSQEQVDEIFRCAALAAADARIPLARMAVTETGMG 60 Query: 61 IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120 ++EDKVIKNHFASEYIYNAYKDEKTCGVL D FGT+TIAEPIGIICGIVPTTNPTSTA Sbjct: 61 VLEDKVIKNHFASEYIYNAYKDEKTCGVLEVDALFGTMTIAEPIGIICGIVPTTNPTSTA 120 Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180 IFK+LISLKTRN IIFSPHPRA+ +T +AA IVL+AA+AAGAPKD+IGWID PSVELSNA Sbjct: 121 IFKALISLKTRNGIIFSPHPRARKSTCEAARIVLEAAVAAGAPKDIIGWIDAPSVELSNA 180 Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240 LMHH D NLILATGGPGMVKAAYSSGKPAIGVGAGNTPVV+DETADIKR VAS+LMSKTF Sbjct: 181 LMHHKDTNLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVVDETADIKRMVASILMSKTF 240 Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300 DNGV+CASEQSV++VD VY+ ++RF GGY+L KE +AV+ VIL NG LNA IVGQ Sbjct: 241 DNGVVCASEQSVIIVDEVYEQAKDRFVRAGGYVLNKKETEAVRKVILVNGGLNANIVGQS 300 Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360 A +IAE+AG +VP TK+LIGEV V + E FAHEKLSPTLAMYRAKDF DAVEKA LV Sbjct: 301 AARIAEMAGITVPSYTKVLIGEVASVGDEEAFAHEKLSPTLAMYRAKDFYDAVEKAVALV 360 Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420 A+GGIGHTS LYT+QD Q R++YFG KMKTARILINTP+SQGGIGDLYNFKLAPSLTLG Sbjct: 361 ALGGIGHTSALYTNQDMQDERIAYFGDKMKTARILINTPSSQGGIGDLYNFKLAPSLTLG 420 Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPK+IYFRRG LP AL ++ +G K Sbjct: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKNIYFRRGCLPFALRDL--EGKK 478 Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540 RA IVT FLFNNGY D+ +LK G+E EVFFEVEADPTL +VRKG N FKPDVI Sbjct: 479 RASIVTGSFLFNNGYCDETIRILKQMGMEVEVFFEVEADPTLEVVRKGVHALNVFKPDVI 538 Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600 IALGGGSPMDAAKIMWVMYEHPE HFE+LALRFMDIRKRIYKFPKMG+KA+++A+ TTSG Sbjct: 539 IALGGGSPMDAAKIMWVMYEHPEVHFEDLALRFMDIRKRIYKFPKMGIKAELVAIPTTSG 598 Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660 TGSEVTPFAVVTD+ TG KYP+ADY LTP+MAI+DA+LVMDMPKSL AFGG+DAVTHA+E Sbjct: 599 TGSEVTPFAVVTDEKTGTKYPIADYELTPNMAIIDADLVMDMPKSLTAFGGIDAVTHALE 658 Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720 AYVSV+A+E+SD QALQAL LLK YLP+SY G+ +P ARE+VH+AATIAG+AFANAFLG Sbjct: 659 AYVSVMANEYSDPQALQALTLLKAYLPSSYANGANDPRAREQVHNAATIAGVAFANAFLG 718 Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780 VCHSMAHKLG++FH+ HGLANALLI NVIRYNA D PTKQTAFSQYDRPQA+ RYA+IA+ Sbjct: 719 VCHSMAHKLGAEFHLAHGLANALLITNVIRYNAVDIPTKQTAFSQYDRPQAKCRYADIAE 778 Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840 HLGL D K+E L+AW+ LK LGIP SI+ AGV EA FL+ +D+++E+AFDDQ Sbjct: 779 HLGLGGKDD--DEKVEALIAWVNELKNVLGIPASIQAAGVPEALFLSKLDEVAEEAFDDQ 836 Query: 841 CTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA 891 CTGANPRYPLISELKQ+LLD+YYGR YVE + EA AKA+ AK +A Sbjct: 837 CTGANPRYPLISELKQLLLDSYYGRTYVESYEREQVEAVVAKAQAAAKAAA 887 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: 1918 Number of extensions: 59 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: 891 Length of database: 888 Length adjustment: 43 Effective length of query: 848 Effective length of database: 845 Effective search space: 716560 Effective search space used: 716560 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