Align aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized)
to candidate 8501604 DvMF_2322 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)
Query= CharProtDB::CH_018413 (862 letters) >FitnessBrowser__Miya:8501604 Length = 904 Score = 962 bits (2488), Expect = 0.0 Identities = 479/859 (55%), Positives = 637/859 (74%), Gaps = 8/859 (0%) Query: 9 LDEKLKVIKEAQKKFSCYSQEMVDEIFRNAAMAAIDARIELAKAAVLETGMGLVEDKVIK 68 +D+ + + EAQ+ F+ ++Q+ VD IF AA AA RI LA+ AV ETGMG++EDKVIK Sbjct: 36 VDDIVTRVNEAQRAFANFTQQQVDAIFHAAAAAATAQRIHLARMAVQETGMGILEDKVIK 95 Query: 69 NHFAGEYIYNKYKDEKTCGIIERNEPYGITKIAEPIGVVAAIIPVTNPTSTTIFKSLISL 128 NHFA EYIYNKYKD+KTCG+I + YG ++A PIGV+A IIP TNPTSTTIFK+L++L Sbjct: 96 NHFASEYIYNKYKDDKTCGVIRDDPAYGYREVAAPIGVIAGIIPTTNPTSTTIFKALLAL 155 Query: 129 KTRNGIFFSPHPRAKKSTILAAKTILDAAVKSGAPENIIGWIDEPSIELTQYLMQKADIT 188 KTRNGI F+PHPRA KST+ AA+ + +AAV +GAP IIGW++ P+ +LT+ LMQ + Sbjct: 156 KTRNGIIFAPHPRAAKSTVEAARIVHEAAVAAGAPRGIIGWVEAPTPDLTRQLMQHRGVA 215 Query: 189 L--ATGGPSLVKSAYSSGKPAIGVGPGNTPVIIDESAHIKMAVSSIILSKTYDNGVICAS 246 L ATGGP +V +AYSSGKPAIGVG GNTPV++D SA++KMAV+SIILSKT+DNG+ICAS Sbjct: 216 LILATGGPGMVHAAYSSGKPAIGVGAGNTPVVVDASANVKMAVNSIILSKTFDNGMICAS 275 Query: 247 EQSVIVLKSIYNKVKDEFQERGAYIIKKNELDKVREVIFKDGSVNPKIVGQSAYTIAAMA 306 EQ+VIV + + VK EF RG + E + + V+F DG +N IVG+SA IAAMA Sbjct: 276 EQAVIVEDAAADAVKAEFAARGCHFASPQEAEALAGVVFTDGRLNAAIVGRSAAEIAAMA 335 Query: 307 GIKVPKTTRILIGEVTSLGEEEPFAHEKLSPVLAMYEADNFDDALKKAVTLINLGGLGHT 366 GI VP TT+ILI E ++ +PFAHEKLSPVL Y A +F A+ A L+ LGG GHT Sbjct: 336 GITVPPTTKILIAERDAIDPLDPFAHEKLSPVLGFYRAPDFAAAVDMAQRLVELGGAGHT 395 Query: 367 SGIYADEIKARDKIDRFSSAMKTVRTFVNIPTSQGASGDLYNFRIPPSFTLGCGFWGGNS 426 S +Y +E R++I F + + T RT VN+P+SQGA GD+YNF + PS TLGCG WG NS Sbjct: 396 SVLYTNEAN-RERIVHFQNVLTTGRTLVNMPSSQGAIGDVYNFELAPSLTLGCGSWGDNS 454 Query: 427 VSENVGPKHLLNIKTVAERRENMLWFRVPHKVYFKFGCLQFALKDLKDLKKKRAFIVTDS 486 VSEN+G KHL+N+KTVAERRENMLWFRVP K+YFK G L+ AL+D++D +KRAFIVTD Sbjct: 455 VSENIGVKHLMNVKTVAERRENMLWFRVPPKIYFKMGALRLALEDMRD--RKRAFIVTDR 512 Query: 487 DPYNLNYVDSIIKILEHLDIDFKVFNKVGREADLKTIKKATEEMSSFMPDTIIALGGTPE 546 +L +V + +LE L I F+VF+ V + DL A + + +F PD IALGG Sbjct: 513 TMEDLGHVGKVTAVLEKLGIQFRVFSDVKPDPDLSGTYAALDSIRAFRPDMFIALGGGSP 572 Query: 547 MSSAKLMWVLYEHPEVKFEDLAIKFMDIRKRIYTFPKLGKKAMLVAITTSAGSGSEVTPF 606 M +AK+MW++YE P++KFE+++++FMDIRKR++ FP LGKKA++VA+ T++G+GSEVTPF Sbjct: 573 MDAAKIMWLMYEQPDLKFEEISLRFMDIRKRVHAFPALGKKAVMVAVPTTSGTGSEVTPF 632 Query: 607 ALVTDNNTGNKYMLADYEMTPNMAIVDAELMMKMPKGLTAYSGIDALVNSIEAYTSVYAS 666 A++TD+ TG KY +ADYE+TP+MAIVD E +M MPK LTA+SG+DAL +++EA+TS YA+ Sbjct: 633 AVITDDATGMKYPIADYELTPDMAIVDPEFVMDMPKTLTAHSGLDALTHAVEAFTSTYAN 692 Query: 667 EYTNGLALEAIRLIFKYLPEAYKNGRTNEKAREKMAHASTMAGMASANAFLGLCHSMAIK 726 +++G ALEA+RL+FKYL AY +G + AREKM +A T+AGMA ANAFLG+CHSMA K Sbjct: 693 NFSDGNALEAVRLVFKYLRRAYNDGARDVMAREKMHYAGTIAGMAFANAFLGVCHSMAHK 752 Query: 727 LSSEHNIPSGIANALLIEEVIKFNAVDNPVKQAPCPQYKYPNTIFRYARIADYIKLG--- 783 L + ++P G+ANALL+ VI++NA D P KQ PQY+YP RYARIAD + L Sbjct: 753 LGAAFHMPHGLANALLLSHVIEYNATDTPTKQGLMPQYRYPFVKGRYARIADMLGLTEGC 812 Query: 784 GNTDEEKVDLLINKIHELKKALNIPTSIKDAGVLEENFYSSLDRISELALDDQCTGANPR 843 G+ + KV L+ I +LK LN+P S+++AG+ E +F +D ++E A DDQCTG NPR Sbjct: 813 GDDRDRKVARLVQAIEQLKADLNVPGSLREAGIAEADFLERVDLLAEQAFDDQCTGGNPR 872 Query: 844 FPLTSEIKEMYINCFKKQP 862 +PL +EI+E+Y+ + P Sbjct: 873 YPLIAEIRELYLKAYYGAP 891 Lambda K H 0.317 0.134 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: 1844 Number of extensions: 79 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: 862 Length of database: 904 Length adjustment: 43 Effective length of query: 819 Effective length of database: 861 Effective search space: 705159 Effective search space used: 705159 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 (21.6 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