Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate SM_b21301 SM_b21301 ly membrane-anchored aldehyde dehydrogenase
Query= reanno::BFirm:BPHYT_RS25810 (796 letters) >FitnessBrowser__Smeli:SM_b21301 Length = 794 Score = 1087 bits (2812), Expect = 0.0 Identities = 549/797 (68%), Positives = 630/797 (79%), Gaps = 4/797 (0%) Query: 1 MSVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQ 60 MSVA +F M YGPAPE D ARAWL +HE GHFI GA+ A+G+ F + PATG+ Sbjct: 1 MSVATFFDEMSYGPAPEADTEARAWLTRHEGKLGHFINGAFVGSASGKSFDTFEPATGKL 60 Query: 61 LAQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDN 120 LA++A G D++AAVAAAR AQ W L G RARHLYALAR++QRH+RL AV+EALDN Sbjct: 61 LAKIAHGGRDDVNAAVAAARKAQGPWAKLSGHARARHLYALARLIQRHARLIAVVEALDN 120 Query: 121 GKPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIA 180 GKPIRETRDID+PL ARHF HHAGWAQLQE+EFAD P+GVVGQ++PWNFP LMLAWK+A Sbjct: 121 GKPIRETRDIDIPLAARHFYHHAGWAQLQETEFADQVPVGVVGQVIPWNFPFLMLAWKVA 180 Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKI 240 PA+A GN V+LKPAE+TPLTALLFAELA AGLP GVLNVVTG+G TGA +VEH +DKI Sbjct: 181 PALALGNSVILKPAEFTPLTALLFAELAAAAGLPPGVLNVVTGEGETGALIVEHEDIDKI 240 Query: 241 AFTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300 AFTGSTEVGRLIR TAGSGKSLTLELGGKSPFIVFDDAD+D AVEGVVDAIWFNQGQVC Sbjct: 241 AFTGSTEVGRLIREKTAGSGKSLTLELGGKSPFIVFDDADIDAAVEGVVDAIWFNQGQVC 300 Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLVETGRR 360 CAGSRLLVQEG+ F +LKRRMETLRVG LDK+ID+ AIV PVQL+RI+ LV G Sbjct: 301 CAGSRLLVQEGVAPVFHDRLKRRMETLRVGHPLDKAIDMAAIVAPVQLQRIEELVAKGVA 360 Query: 361 EGCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN 420 EG S+ Q P +P GG FF PTL+TGV P S +A EEIFGPV V+M+FRTP+EAI LAN Sbjct: 361 EGASMHQ-PKIELPKGGSFFRPTLLTGVQPTSVVATEEIFGPVAVSMTFRTPEEAIQLAN 419 Query: 421 NSRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGREGGREG 480 +SRYGLAASVWSETIG AL VA +LA+GVVW+NATNLFDA+ GFGG RESG+GREGGREG Sbjct: 420 HSRYGLAASVWSETIGLALHVAAKLAAGVVWVNATNLFDASSGFGGKRESGFGREGGREG 479 Query: 481 IYEYLKPRAWLKLAERRAAQDVVRDAAALDPLSNVTSIDRTAKLFIGGKQARPDSGYSLP 540 YEYLKP+AW+ R AA D V ++DRTAKLF+GGKQARPD YS P Sbjct: 480 CYEYLKPKAWMGRKLRPEHGLPAPKQAAGD--FAVPALDRTAKLFVGGKQARPDGNYSRP 537 Query: 541 VLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFV 600 VL+P G +GEV GNRKDIRNAV AAR A WS A+ HNRAQ+L+Y+AENL+ R EF Sbjct: 538 VLSPKGKVIGEVGEGNRKDIRNAVVAARGASGWSSATAHNRAQILYYIAENLSSRGAEFA 597 Query: 601 RQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGI 660 ++ GA+ A ARAEV+AS+ RLF+Y AWADK++G VH PPLRGVALAM EP GV+G+ Sbjct: 598 GRIAAMTGASAANARAEVEASIARLFSYGAWADKYEGTVHQPPLRGVALAMPEPQGVVGV 657 Query: 661 ACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIVTGE 720 CP EAPLLG VSL AP +A+GNRVV +PSEA PL TDFY V ETSDVP GV+NIVTG Sbjct: 658 ICPPEAPLLGLVSLVAPLIAVGNRVVAVPSEAHPLAATDFYSVLETSDVPPGVINIVTGS 717 Query: 721 RGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDR-ASEGRP 779 L AL H+DVDA+W FGS STLVE+ SVGNLKRTFVDYG+ DW DR A+EG+ Sbjct: 718 AIELAKALAAHNDVDALWAFGSPELSTLVEKLSVGNLKRTFVDYGKAIDWTDRSAAEGQA 777 Query: 780 FLRQAVQVKNIWIPYGD 796 FLR+AV VKNIWIPYG+ Sbjct: 778 FLRRAVDVKNIWIPYGE 794 Lambda K H 0.319 0.135 0.408 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: 1827 Number of extensions: 71 Number of successful extensions: 9 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: 796 Length of database: 794 Length adjustment: 41 Effective length of query: 755 Effective length of database: 753 Effective search space: 568515 Effective search space used: 568515 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.8 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