Align alcohol dehydrogenase / acetaldehyde dehydrogenase (EC 1.2.1.10; EC 1.1.1.1) (characterized)
to candidate 8501604 DvMF_2322 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)
Query= metacyc::GIO2-535-MONOMER (954 letters) >FitnessBrowser__Miya:8501604 Length = 904 Score = 1044 bits (2699), Expect = 0.0 Identities = 525/896 (58%), Positives = 667/896 (74%), Gaps = 14/896 (1%) Query: 52 PKAEAAAPVAAAPATPHAEVKKERAPAT--DEALTELKALLKRAQTAQAQYSTYTQEQVD 109 P A+ A P TP A + +P++ ++T + ++ R AQ ++ +TQ+QVD Sbjct: 5 PNAQGAKPAT----TPDAISLNDISPSSIAPNSIT-VDDIVTRVNEAQRAFANFTQQQVD 59 Query: 110 EIFRAAAEAANAARIPLAKMAVEETRMGVAEDKVVKNHFASEFIYNKYKHTKTCGVIEHD 169 IF AAA AA A RI LA+MAV+ET MG+ EDKV+KNHFASE+IYNKYK KTCGVI D Sbjct: 60 AIFHAAAAAATAQRIHLARMAVQETGMGILEDKVIKNHFASEYIYNKYKDDKTCGVIRDD 119 Query: 170 PAGGIQKVAEPVGVIAGIVPTTNPTSTAIFKSLLSLKTRNALVLCPHPRAAKSTIAAARI 229 PA G ++VA P+GVIAGI+PTTNPTST IFK+LL+LKTRN ++ PHPRAAKST+ AARI Sbjct: 120 PAYGYREVAAPIGVIAGIIPTTNPTSTTIFKALLALKTRNGIIFAPHPRAAKSTVEAARI 179 Query: 230 VRDAAVAAGAPPNIISWVETPSLPVSQALMQATEINLILATGGPAMVRAAYSSGNPSLGV 289 V +AAVAAGAP II WVE P+ +++ LMQ + LILATGGP MV AAYSSG P++GV Sbjct: 180 VHEAAVAAGAPRGIIGWVEAPTPDLTRQLMQHRGVALILATGGPGMVHAAYSSGKPAIGV 239 Query: 290 GAGNTPALIDETADVAMAVSSILLSKTFDNGVICASEQSVVVVAKAYDAVRTEFVRRGAY 349 GAGNTP ++D +A+V MAV+SI+LSKTFDNG+ICASEQ+V+V A DAV+ EF RG + Sbjct: 240 GAGNTPVVVDASANVKMAVNSIILSKTFDNGMICASEQAVIVEDAAADAVKAEFAARGCH 299 Query: 350 FLTEDDKVKVRAGVVVDGKLNPNIVGQSIPKLAALFGIKVPQGTKVLIGEVEKIGPEEAL 409 F + + + V DG+LN IVG+S ++AA+ GI VP TK+LI E + I P + Sbjct: 300 FASPQEAEALAGVVFTDGRLNAAIVGRSAAEIAAMAGITVPPTTKILIAERDAIDPLDPF 359 Query: 410 SQEKLCPILAMYRAPDYDHGVKMACELIMYGGAGHTSVLYTNPLNNAHIQQYQSAVKTVR 469 + EKL P+L YRAPD+ V MA L+ GGAGHTSVLYTN N I +Q+ + T R Sbjct: 360 AHEKLSPVLGFYRAPDFAAAVDMAQRLVELGGAGHTSVLYTNEANRERIVHFQNVLTTGR 419 Query: 470 ILINTPASQGAIGDLYNFHLDPSLTLGCGTWGSTSVSTNVGPQHLLNIKTVTARRENMLW 529 L+N P+SQGAIGD+YNF L PSLTLGCG+WG SVS N+G +HL+N+KTV RRENMLW Sbjct: 420 TLVNMPSSQGAIGDVYNFELAPSLTLGCGSWGDNSVSENIGVKHLMNVKTVAERRENMLW 479 Query: 530 FRVPPKIYFKGGCLEVALTDLRGKSRAFIVTDKPLFDMGYADKVTHILDSINVHHQVFYH 589 FRVPPKIYFK G L +AL D+R + RAFIVTD+ + D+G+ KVT +L+ + + +VF Sbjct: 480 FRVPPKIYFKMGALRLALEDMRDRKRAFIVTDRTMEDLGHVGKVTAVLEKLGIQFRVFSD 539 Query: 590 VTPDPTLACIEAGLKEILEFKPDVIIALGGGSPMDAAKIMWLMYECPDTRFDGLAMRFMD 649 V PDP L+ A L I F+PD+ IALGGGSPMDAAKIMWLMYE PD +F+ +++RFMD Sbjct: 540 VKPDPDLSGTYAALDSIRAFRPDMFIALGGGSPMDAAKIMWLMYEQPDLKFEEISLRFMD 599 Query: 650 IRKRVYEVPELGKKATMVCIPTTSGTGSEVTPFSVVTDERLGAKYPLADYALTPSMAIVD 709 IRKRV+ P LGKKA MV +PTTSGTGSEVTPF+V+TD+ G KYP+ADY LTP MAIVD Sbjct: 600 IRKRVHAFPALGKKAVMVAVPTTSGTGSEVTPFAVITDDATGMKYPIADYELTPDMAIVD 659 Query: 710 PQLVLNMPKKLTAWGGIDALTHALESYVSICATDYTKGLSREAISLLFKYLPRAYANGSN 769 P+ V++MPK LTA G+DALTHA+E++ S A +++ G + EA+ L+FKYL RAY +G+ Sbjct: 660 PEFVMDMPKTLTAHSGLDALTHAVEAFTSTYANNFSDGNALEAVRLVFKYLRRAYNDGAR 719 Query: 770 DYLAREKVHYAATIAGMAFANAFLGICHSMAHKLGAAYHVPHGLANAALISHVIRYNATD 829 D +AREK+HYA TIAGMAFANAFLG+CHSMAHKLGAA+H+PHGLANA L+SHVI YNATD Sbjct: 720 DVMAREKMHYAGTIAGMAFANAFLGVCHSMAHKLGAAFHMPHGLANALLLSHVIEYNATD 779 Query: 830 MPAKQAAFPQYEYPTAKQDYADLANMLGLG---GNTVDEKVIKLIEAVEELKAKVDIPPT 886 P KQ PQY YP K YA +A+MLGL G+ D KV +L++A+E+LKA +++P + Sbjct: 780 TPTKQGLMPQYRYPFVKGRYARIADMLGLTEGCGDDRDRKVARLVQAIEQLKADLNVPGS 839 Query: 887 IKEIFNDPKVDADFLANVDALAEDAFDDQCTGANPRYPLMADLKQLYLDA-HAAPI 941 ++E +ADFL VD LAE AFDDQCTG NPRYPL+A++++LYL A + AP+ Sbjct: 840 LREA---GIAEADFLERVDLLAEQAFDDQCTGGNPRYPLIAEIRELYLKAYYGAPL 892 Lambda K H 0.318 0.133 0.387 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: 1948 Number of extensions: 72 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: 954 Length of database: 904 Length adjustment: 43 Effective length of query: 911 Effective length of database: 861 Effective search space: 784371 Effective search space used: 784371 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: 57 (26.6 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