Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate AZOBR_RS32240 AZOBR_RS32240 acetaldehyde dehydrogenase
Query= CharProtDB::CH_024820 (891 letters) >FitnessBrowser__azobra:AZOBR_RS32240 Length = 886 Score = 1327 bits (3435), Expect = 0.0 Identities = 661/886 (74%), Positives = 766/886 (86%), Gaps = 8/886 (0%) Query: 1 MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60 M VT +A+LN LV RV++AQ+ YA F QE VD+IFR+AALAAA+ARIPLAK+AVAE+ MG Sbjct: 1 MPVTTLADLNDLVLRVREAQKVYAGFPQETVDRIFRSAALAAANARIPLAKLAVAETRMG 60 Query: 61 IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120 ++EDKV+KNHFASEYIYN YKDEKTCG+L ED +G +TIAEP+G+IC IVPTTNPTSTA Sbjct: 61 VMEDKVVKNHFASEYIYNKYKDEKTCGILEEDPEYGIMTIAEPVGLICAIVPTTNPTSTA 120 Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180 IFK+LISLKTRN I+FSPHPRA+ AT +AA IVLQAA+ AGAP D+IGWID+PSV+LSNA Sbjct: 121 IFKALISLKTRNGIVFSPHPRARKATCEAARIVLQAAVEAGAPADIIGWIDEPSVDLSNA 180 Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240 +MHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTP VIDE ADIKRAVAS+LMSKTF Sbjct: 181 VMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPAVIDEFADIKRAVASILMSKTF 240 Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300 DNGV+CASEQS +VVD+VYDAVR+RFA HGG++L G + AV+ V+LKNGALNA IVGQ Sbjct: 241 DNGVVCASEQSAIVVDAVYDAVRDRFAHHGGHILSGTDADAVRKVLLKNGALNADIVGQS 300 Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360 A IA +AG SVP NTK+LI EV V E EPFAHEKLSPTLA+YRA+DF DA +KA LV Sbjct: 301 AGAIAAMAGVSVPANTKVLIAEVEAVTEDEPFAHEKLSPTLALYRARDFMDACDKAAALV 360 Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420 A+GGIGHTS LYTDQD QP R+ +FGQ MKTARILINTP+SQGGIGDLYNF+LAPSLTLG Sbjct: 361 ALGGIGHTSALYTDQDQQPERIRHFGQAMKTARILINTPSSQGGIGDLYNFRLAPSLTLG 420 Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480 CGSWGGNSISENVGP+HLIN+KTVAKRAENMLWHKLPKSIYFRRG LP AL+E+ G K Sbjct: 421 CGSWGGNSISENVGPQHLINRKTVAKRAENMLWHKLPKSIYFRRGCLPFALEEL--RGKK 478 Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540 R LIVTDRFLF NG+ D+ +LK G+ E FFEV ADPTL++VR+G LAN+F+PDVI Sbjct: 479 RCLIVTDRFLFENGHVDETVRILKGLGLAVETFFEVAADPTLAVVRRGLALANAFQPDVI 538 Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600 +ALGGGSPMDAAKIMWVMYE P+ FE+LALRFMDIRKRIY FPK+GVKA+ +AV TTSG Sbjct: 539 LALGGGSPMDAAKIMWVMYEAPDVAFEDLALRFMDIRKRIYTFPKLGVKAQFVAVPTTSG 598 Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660 TGSEVTPFAVVTD+ TG KYP+ADY LTP+MAI+DANLVMDMPK L A GG+DAVTHA+E Sbjct: 599 TGSEVTPFAVVTDERTGIKYPIADYELTPNMAIIDANLVMDMPKGLTAAGGIDAVTHALE 658 Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720 AYVSVLA+E++DGQALQALKLLKE+LP++Y G K+P ARE+VHSAAT+AGIAFANAFLG Sbjct: 659 AYVSVLANEYTDGQALQALKLLKEHLPSAYANGGKDPKAREQVHSAATLAGIAFANAFLG 718 Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780 VCHSMAHKLG++FH+PHG+ANALLI NVIRYNA D PTKQTAFSQYDRP+ RYAEIA Sbjct: 719 VCHSMAHKLGAEFHLPHGVANALLIANVIRYNAADIPTKQTAFSQYDRPKGVARYAEIAR 778 Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840 HLGL G R ++E L+AW+E LK L IP SI+ AGV EA+FLA +D ++E AFDDQ Sbjct: 779 HLGLG--GSRDHERVETLVAWVEELKRTLDIPASIQAAGVPEAEFLARLDAIAEAAFDDQ 836 Query: 841 CTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKK 886 CTGANPR+PL++E++Q+LLD+YYGR Y EG A++E AKAE+K Sbjct: 837 CTGANPRFPLVAEIRQLLLDSYYGRAYAEG---AERE-PDAKAERK 878 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: 1905 Number of extensions: 63 Number of successful extensions: 5 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: 886 Length adjustment: 43 Effective length of query: 848 Effective length of database: 843 Effective search space: 714864 Effective search space used: 714864 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 Apr 09 2024. 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