Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate 5209439 Shew_1910 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)
Query= CharProtDB::CH_024820 (891 letters) >FitnessBrowser__PV4:5209439 Length = 872 Score = 1323 bits (3425), Expect = 0.0 Identities = 662/870 (76%), Positives = 754/870 (86%), Gaps = 5/870 (0%) Query: 1 MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60 M V+N EL+ LVERV KAQ ++A+F+QEQVDKIFRAAALAAADARI LAKMA E+GMG Sbjct: 1 MTVSNQQELDQLVERVAKAQAQFANFSQEQVDKIFRAAALAAADARISLAKMAANETGMG 60 Query: 61 IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120 ++EDKVIKNHFASEYIYN YKD+KTCG+L ED TFGTITIAEP+G+ICGIVPTTNPTSTA Sbjct: 61 VLEDKVIKNHFASEYIYNKYKDDKTCGILEEDPTFGTITIAEPVGLICGIVPTTNPTSTA 120 Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180 IFK+LISLKTRN IIFSPHPRAK +T AA +VL+AA+ AGAPKD+IGWID+PSV LSN Sbjct: 121 IFKALISLKTRNGIIFSPHPRAKVSTTTAARLVLEAAVEAGAPKDIIGWIDEPSVALSNQ 180 Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240 LM H INLILATGGPGMVKAAYSSGKPAIGVGAGNTP+VIDETADIKRAV+S+LMSKTF Sbjct: 181 LMTHDKINLILATGGPGMVKAAYSSGKPAIGVGAGNTPIVIDETADIKRAVSSILMSKTF 240 Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300 DNGV+CASEQ+VVVVD+VYDAV+ERFA+HGGY+L KE KA+Q VILKNGALNA IVGQ Sbjct: 241 DNGVVCASEQAVVVVDAVYDAVKERFASHGGYMLSSKEAKAMQKVILKNGALNADIVGQS 300 Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360 A IA +A VP +TK+LIG+ T + ESE FAHEKLSP LAMYRA DF+DA+ KAE LV Sbjct: 301 AATIAAMANIKVPASTKVLIGQATEISESEAFAHEKLSPLLAMYRASDFDDALNKAEALV 360 Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420 +GGIGHTS LYTDQD Q RV FG +MKTARILINTPASQGGIGDLYNFKLAPSLTLG Sbjct: 361 TLGGIGHTSGLYTDQDTQTERVRTFGFRMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420 Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480 CGSWGGNSISENVGP HLINKKTVAKRAENMLWHKLP SIYFRRGSLPIAL+E+ K Sbjct: 421 CGSWGGNSISENVGPSHLINKKTVAKRAENMLWHKLPSSIYFRRGSLPIALEEL--SDKK 478 Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540 RALIVTD++LFNNGY D+ +LK+ G+ETEVF+EVEADPTL+IV +GA +A SF+PDVI Sbjct: 479 RALIVTDKYLFNNGYCDETIKILKSQGLETEVFYEVEADPTLAIVNQGASVAKSFQPDVI 538 Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600 IALGGGSPMDAAKI+WVMYEHPE F +LALRFMDIRKRIYKFPK+G KAKM+A+ TTSG Sbjct: 539 IALGGGSPMDAAKIIWVMYEHPEVDFADLALRFMDIRKRIYKFPKLGKKAKMVAIPTTSG 598 Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660 TGSEVTPFAVVTD+ TG KYP+ADY LTP+MAIVD NLVMDMPKSL AFGG+DA+THA+E Sbjct: 599 TGSEVTPFAVVTDEQTGMKYPIADYELTPNMAIVDPNLVMDMPKSLTAFGGIDAITHALE 658 Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720 AYVSV+A+E+SDGQALQAL LL +YLP SY G++ PVARE+VH+ ATIAGIAFANAFLG Sbjct: 659 AYVSVMANEYSDGQALQALDLLVKYLPDSYALGAQAPVAREKVHNGATIAGIAFANAFLG 718 Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780 +CHSMAHKLG++FH+ HGLANALLI NVIR+NA D PTKQ AFSQYDRP+A RYA+IA+ Sbjct: 719 ICHSMAHKLGAEFHLAHGLANALLISNVIRFNATDLPTKQAAFSQYDRPKALCRYAKIAE 778 Query: 781 HL---GLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAF 837 HL G + G K+E LL ++ LK +GIP SI+EAGV EADF A +D+L+EDAF Sbjct: 779 HLKLKGATGEGISDEEKVEALLEKIDELKKTIGIPASIQEAGVNEADFFAKLDELAEDAF 838 Query: 838 DDQCTGANPRYPLISELKQILLDTYYGRDY 867 DDQCTGANPRYPLI+ELK IL ++YG+ Y Sbjct: 839 DDQCTGANPRYPLIAELKAILTASFYGKKY 868 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: 1817 Number of extensions: 58 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: 872 Length adjustment: 43 Effective length of query: 848 Effective length of database: 829 Effective search space: 702992 Effective search space used: 702992 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 17 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