Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_011652277.1 RL_RS14170 aldehyde dehydrogenase family protein
Query= reanno::BFirm:BPHYT_RS25810 (796 letters) >NCBI__GCF_000009265.1:WP_011652277.1 Length = 795 Score = 1086 bits (2809), Expect = 0.0 Identities = 541/797 (67%), Positives = 636/797 (79%), Gaps = 3/797 (0%) Query: 1 MSVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQ 60 M+VA+YF M YGPAPE D AR WLA+H GFGHFI GA+ A+G+ F + PATG+ Sbjct: 1 MTVAKYFDEMSYGPAPESDIEARDWLARHASGFGHFINGAFVPSASGKNFDTFEPATGKV 60 Query: 61 LAQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDN 120 LA++A G A D+D AVAAAR AQ W L G RARHLYALARM+QRH+RL AV+EA+DN Sbjct: 61 LAKLANGGATDVDNAVAAARKAQASWARLPGHARARHLYALARMIQRHARLIAVVEAIDN 120 Query: 121 GKPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIA 180 GKPIRETRD+DVPL ARHF HHAGWAQ+Q++EFAD+ P+GVVGQI+PWNFP LMLAWK+A Sbjct: 121 GKPIRETRDLDVPLAARHFYHHAGWAQIQDTEFADHVPVGVVGQIIPWNFPFLMLAWKVA 180 Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKI 240 PA+A GN V+LKPAE+T LTALLFAELA AGLP GVLN+VTG+G TGA LV H +DKI Sbjct: 181 PALALGNAVILKPAEFTSLTALLFAELASAAGLPPGVLNIVTGEGETGALLVGHEDIDKI 240 Query: 241 AFTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300 AFTGSTEVGR+IR TAGSGKSLTLELGGKSPF+VFDDAD+DGAVEG VDAIWFNQGQVC Sbjct: 241 AFTGSTEVGRVIRERTAGSGKSLTLELGGKSPFVVFDDADIDGAVEGAVDAIWFNQGQVC 300 Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLVETGRR 360 CAGSRLLVQEGI F +LKRRMETLRVG LDK ID+GAI+ PVQL RI++LV+ G Sbjct: 301 CAGSRLLVQEGIADLFHERLKRRMETLRVGQPLDKCIDMGAIIAPVQLTRIEALVKKGVS 360 Query: 361 EGCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN 420 EG ++ Q+ +P GG F+PPTL++GV P S +A EEIFGPV V+M+FRTP+EAI LAN Sbjct: 361 EGATLHQA-KIDLPKGGSFYPPTLLSGVQPTSIVATEEIFGPVAVSMTFRTPEEAIQLAN 419 Query: 421 NSRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGREGGREG 480 ++RYGLAASVWSETIG AL+VA +LA+GVVW+NATNLFDAAVGFGG RESG+GREGGREG Sbjct: 420 HTRYGLAASVWSETIGLALNVAAKLAAGVVWVNATNLFDAAVGFGGKRESGFGREGGREG 479 Query: 481 IYEYLKPRAWLKLAERRAAQDVVRDAAALDPLSNVTSIDRTAKLFIGGKQARPDSGYSLP 540 YEYLKP+AW+ + RAA + + + SIDRTAKLFIGGKQARPD YS Sbjct: 480 CYEYLKPKAWVG-RKTRAAMPALSQVKPVAGDFALPSIDRTAKLFIGGKQARPDGNYSRV 538 Query: 541 VLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFV 600 + +P G +GEV GNRKDIRNAV AA+AA WS A+THNRAQ+L+Y+AENL+ RADEF Sbjct: 539 IASPKGKAIGEVGEGNRKDIRNAVVAAQAASAWSNATTHNRAQILYYIAENLSGRADEFA 598 Query: 601 RQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGI 660 ++ GA+ A A AEVDA++ RLFTYAAWADK++G +H PPLRGVALAM E +GV+GI Sbjct: 599 SRITAMTGASAANANAEVDAAISRLFTYAAWADKYEGGIHQPPLRGVALAMPEAIGVVGI 658 Query: 661 ACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIVTGE 720 CP EAPLLGF+SL AP +A GNRVV +PSEA PL+ TDFY V ETSD+P GV+NIVTG Sbjct: 659 ICPPEAPLLGFISLIAPLIATGNRVVAVPSEAFPLSATDFYSVLETSDLPAGVVNIVTGS 718 Query: 721 RGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDRAS-EGRP 779 L L H+DVDA+W FGSA ST VE+ S GNLKRTFVD G+ DW DRA+ EG Sbjct: 719 AIELAKILAAHNDVDALWAFGSAELSTTVEKLSSGNLKRTFVDNGKATDWMDRAAGEGAL 778 Query: 780 FLRQAVQVKNIWIPYGD 796 +LR+AV VKNIWIPYG+ Sbjct: 779 YLRRAVDVKNIWIPYGE 795 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: 1808 Number of extensions: 65 Number of successful extensions: 8 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: 795 Length adjustment: 41 Effective length of query: 755 Effective length of database: 754 Effective search space: 569270 Effective search space used: 569270 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 24 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