Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate 3609634 Dshi_3017 aldehyde dehydrogenase (RefSeq)
Query= reanno::BFirm:BPHYT_RS25810 (796 letters) >FitnessBrowser__Dino:3609634 Length = 780 Score = 967 bits (2499), Expect = 0.0 Identities = 495/795 (62%), Positives = 588/795 (73%), Gaps = 16/795 (2%) Query: 1 MSVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQ 60 M+V E F +MEYGPAPEDD PA+AWL +H FG FIGG + AP G+ FA+ PA G + Sbjct: 1 MTVKEIFETMEYGPAPEDDGPAQAWLDRHGRRFGVFIGGTFQAP--GKTFATRNPARGTE 58 Query: 61 LAQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDN 120 LAQV QG ADI+AAV AAR AQP W LGG G AR LYA+AR++Q+HSRLFAVLE LDN Sbjct: 59 LAQVTQGTEADIEAAVTAARRAQPAWARLGGQGWARVLYAIARLLQKHSRLFAVLETLDN 118 Query: 121 GKPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIA 180 GKPIRE+RDID+PL RHF +HAG A L E E D P+GV GQIVPWNFPLLMLAWKIA Sbjct: 119 GKPIRESRDIDIPLAQRHFYYHAGMAALMEDELPDRVPVGVCGQIVPWNFPLLMLAWKIA 178 Query: 181 PAIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKI 240 PA+A GN VVLKPAE+TPLTALLFAE+ AG+P GV+N+VTGDG TGAALV HP VDKI Sbjct: 179 PALAMGNTVVLKPAEWTPLTALLFAEICGEAGVPPGVVNIVTGDGATGAALVSHPGVDKI 238 Query: 241 AFTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVC 300 AFTGST+VGR IR ATAG+GK+LTLELGGKSP++VF+DADLD AVEG+VDAIWFNQGQVC Sbjct: 239 AFTGSTDVGREIRRATAGTGKALTLELGGKSPYVVFEDADLDSAVEGLVDAIWFNQGQVC 298 Query: 301 CAGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLVETGRR 360 CAGSRLLVQEGI F AKL+ RM TLR+G LDK ID+GA+VDP ++ +V Sbjct: 299 CAGSRLLVQEGIAEAFYAKLRARMATLRIGDPLDKCIDVGAMVDPAHCAKVAEMVAGSNG 358 Query: 361 EGCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIALAN 420 E T+P+ G F+PPTL+TG+ PA L ++EIFGPVLV +FRTP EA+ +AN Sbjct: 359 E-----VHQPGTVPAEGAFYPPTLITGLEPADPLMRDEIFGPVLVATTFRTPAEAVEVAN 413 Query: 421 NSRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGREGGREG 480 +RYGLAA++WSE I RALD+AP+LA+GVVW+NATNLFDAA GFGG RESG+GREGG EG Sbjct: 414 ATRYGLAATLWSENINRALDIAPKLAAGVVWVNATNLFDAAAGFGGVRESGFGREGGWEG 473 Query: 481 IYEYLKPRAWLKLAERRAAQDVVRDAAALDPLSNVTSIDRTAKLFIGGKQARPDSGYSLP 540 + Y K A K AA + AA P +DRTAK++IGGKQARPDSGYS P Sbjct: 474 LRAYTKQAAPPKALVPVAA---IPAPAAPKP----GGLDRTAKMYIGGKQARPDSGYSRP 526 Query: 541 VLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVRADEFV 600 V +P G +G G+RKDIRNAVEAA A W + + H RAQ+L+Y+AENL+ R +EF Sbjct: 527 VWSPKGVLLGHAPEGSRKDIRNAVEAATGAASWGRTTGHLRAQILYYVAENLSARTEEFA 586 Query: 601 RQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVIGI 660 ++ G+ A AEV A++ RLFTYAAWADK+DGAV P+RGVALAM EP+GVIG Sbjct: 587 TRIAEMTGSRVPRAEAEVSAAIDRLFTYAAWADKYDGAVKPVPIRGVALAMPEPVGVIGA 646 Query: 661 ACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIVTGE 720 PD+APLLG VS+ ALAMGNR+V++PSE PL TD YQV +TSDVP GV+NIVTG Sbjct: 647 FAPDDAPLLGAVSILGAALAMGNRLVLVPSEPFPLAATDLYQVLDTSDVPAGVVNIVTGA 706 Query: 721 RGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDRASEGRPF 780 AL L H VDAVW F A ST +E E+ GNLKRT+V++GR DW + R F Sbjct: 707 HEALAKPLASHLGVDAVWSFSGADISTTIEAEAAGNLKRTWVNHGRARDWMQ--VDARSF 764 Query: 781 LRQAVQVKNIWIPYG 795 L QA + K IW+PYG Sbjct: 765 LAQATETKTIWVPYG 779 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: 1793 Number of extensions: 81 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: 780 Length adjustment: 41 Effective length of query: 755 Effective length of database: 739 Effective search space: 557945 Effective search space used: 557945 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