Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate 201293 SO2136 aldehyde-alcohol dehydrogenase (NCBI ptt file)
Query= CharProtDB::CH_024820 (891 letters) >FitnessBrowser__MR1:201293 Length = 866 Score = 1352 bits (3500), Expect = 0.0 Identities = 677/869 (77%), Positives = 760/869 (87%), Gaps = 4/869 (0%) Query: 1 MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG 60 M VTN +L+ +VERV +AQ EYASF+Q QVD IFRAAALAAADARI LAKMA AE+ MG Sbjct: 1 MTVTNAQKLDLMVERVARAQAEYASFSQAQVDAIFRAAALAAADARISLAKMAAAETRMG 60 Query: 61 IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA 120 ++EDKVIKNHFASEYIYN YKDEKTCG+LSED TFGTITIAEP+GIICGIVPTTNPTSTA Sbjct: 61 VIEDKVIKNHFASEYIYNKYKDEKTCGILSEDPTFGTITIAEPVGIICGIVPTTNPTSTA 120 Query: 121 IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA 180 IFK+LISLKTRNAIIFSPHPRAK +T AA +VL AAIAAGAPKD+IGWID+PSV LSN Sbjct: 121 IFKALISLKTRNAIIFSPHPRAKVSTTTAAKLVLDAAIAAGAPKDIIGWIDEPSVALSNQ 180 Query: 181 LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF 240 LM HP +NLILATGGPGMVKAAYSSGKPAIGVGAGNTP+VIDETADIKRAV+S+LMSKTF Sbjct: 181 LMTHPKVNLILATGGPGMVKAAYSSGKPAIGVGAGNTPIVIDETADIKRAVSSILMSKTF 240 Query: 241 DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP 300 DNGV+CASEQ+V+VVDS+Y+ V+ERFATHGGYLL + +A+Q VILKNG LNA IVGQ Sbjct: 241 DNGVVCASEQAVIVVDSIYEQVKERFATHGGYLLNAAQTEAMQQVILKNGGLNADIVGQS 300 Query: 301 AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV 360 A IA++AG VP TK+LIGEVT + E+E FAHEKLSP L MYRA DF DAV+KAE LV Sbjct: 301 AATIAQMAGIEVPHTTKVLIGEVTDISETEAFAHEKLSPLLGMYRAADFNDAVDKAETLV 360 Query: 361 AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420 A+GGIGHTS LYTDQD Q RV FG +MKTARILINTPASQGGIGDLYNFKLAPSLTLG Sbjct: 361 ALGGIGHTSGLYTDQDTQTERVKSFGFRMKTARILINTPASQGGIGDLYNFKLAPSLTLG 420 Query: 421 CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK 480 CGSWGGNSISENVGP HLINKKTVAKRAENMLWHKLP SIYFRRGSLPIAL+E+ K Sbjct: 421 CGSWGGNSISENVGPSHLINKKTVAKRAENMLWHKLPSSIYFRRGSLPIALEEL--SDKK 478 Query: 481 RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI 540 RALIVTD FLFN GY D+ +LKA G+ETEVF+EVEADPTL+ VR+GA++ANSFKPDVI Sbjct: 479 RALIVTDPFLFNQGYCDETLKILKAQGLETEVFYEVEADPTLATVRQGAKVANSFKPDVI 538 Query: 541 IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG 600 IALGGGSPMDAAKI+WVMYEHP+ F +LALRFMDIRKRIYKFPKMGVKA M+A+ TTSG Sbjct: 539 IALGGGSPMDAAKIIWVMYEHPDVDFADLALRFMDIRKRIYKFPKMGVKATMVAIPTTSG 598 Query: 601 TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME 660 TGSEVTPFAVVTD+ TG+KYP+ADY LTP+MAIVD NLVMDMPKSL AFGG+DA+THA+E Sbjct: 599 TGSEVTPFAVVTDEQTGKKYPIADYQLTPNMAIVDPNLVMDMPKSLTAFGGIDAITHALE 658 Query: 661 AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG 720 AYVSV+A+E+SDGQALQAL LL +YLP +Y G+ +P+ARE+VH+ ATIAGIAFANAFLG Sbjct: 659 AYVSVMANEYSDGQALQALDLLCKYLPDAYQLGAASPIAREKVHNGATIAGIAFANAFLG 718 Query: 721 VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD 780 +CHSMAHKLG++FH+ HGLANALLI NVIR+NA D PTKQ AFSQYDRP+A RYA IAD Sbjct: 719 ICHSMAHKLGAEFHLAHGLANALLISNVIRFNATDLPTKQAAFSQYDRPKALCRYAAIAD 778 Query: 781 HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ 840 HL L G+ A K+EKLL +E LK LGIP SI+EAGV EADFLA +D L+EDAFDDQ Sbjct: 779 HLALG--GNSDAQKVEKLLEKIEQLKKTLGIPASIQEAGVNEADFLAKLDMLAEDAFDDQ 836 Query: 841 CTGANPRYPLISELKQILLDTYYGRDYVE 869 CTGANPRYPLISELKQ+LLD+YYGR + E Sbjct: 837 CTGANPRYPLISELKQLLLDSYYGRPFTE 865 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: 1847 Number of extensions: 63 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: 866 Length adjustment: 43 Effective length of query: 848 Effective length of database: 823 Effective search space: 697904 Effective search space used: 697904 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