Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_011810430.1 VEIS_RS13090 aldehyde dehydrogenase family protein
Query= reanno::BFirm:BPHYT_RS25810 (796 letters) >NCBI__GCF_000015565.1:WP_011810430.1 Length = 798 Score = 929 bits (2402), Expect = 0.0 Identities = 487/799 (60%), Positives = 573/799 (71%), Gaps = 7/799 (0%) Query: 2 SVAEYFSSMEYGPAPEDDQPARAWLAQHEDGFGHFIGGAWHAPAAGERFASNAPATGEQL 61 +VA+ +M+YGP E P +WL H F HFI G + APA E F PAT E+L Sbjct: 3 TVADILRTMDYGPCLEAAAPVHSWLDAHAHSFRHFIHGEFVAPAQNEYFEVFNPATEERL 62 Query: 62 AQVAQGDAADIDAAVAAARAAQPGWLALGGAGRARHLYALARMVQRHSRLFAVLEALDNG 121 A+VA G ADID AVAAAR A P W L G RAR+LYA+AR +Q+H+R FAVLE +DNG Sbjct: 63 ARVAHGSDADIDQAVAAARQALPAWSGLSGHQRARYLYAIARHLQKHARFFAVLETMDNG 122 Query: 122 KPIRETRDIDVPLVARHFLHHAGWAQLQESEFADYAPLGVVGQIVPWNFPLLMLAWKIAP 181 K IRE+RDID+PLV RHF HHAGWAQL +SEF + +GV GQIVPWNFPLLMLAWK+AP Sbjct: 123 KTIRESRDIDIPLVVRHFYHHAGWAQLLDSEFPAHQAVGVCGQIVPWNFPLLMLAWKVAP 182 Query: 182 AIATGNCVVLKPAEYTPLTALLFAELAHRAGLPAGVLNVVTGDGRTGAALVEHPQVDKIA 241 A+A GN VVLKPAE+TPLTAL FAEL GLPAGVLN+VTGDG TGA+LV H VDKIA Sbjct: 183 ALAAGNTVVLKPAEFTPLTALAFAELCVEVGLPAGVLNIVTGDGHTGASLVNHAGVDKIA 242 Query: 242 FTGSTEVGRLIRSATAGSGKSLTLELGGKSPFIVFDDADLDGAVEGVVDAIWFNQGQVCC 301 FTGST VGRLIR ATAG+ K L+LELGGKSPFIVFDDADLD AVEGVVD+IWFNQGQVCC Sbjct: 243 FTGSTAVGRLIRRATAGTDKKLSLELGGKSPFIVFDDADLDAAVEGVVDSIWFNQGQVCC 302 Query: 302 AGSRLLVQEGIEARFIAKLKRRMETLRVGTSLDKSIDLGAIVDPVQLERIQSLVETGRRE 361 AGSR+LVQE + ARF KL+ RM LR+G LDKS D+GAIVD VQL+RI+ +VE+GR + Sbjct: 303 AGSRILVQESVAARFGDKLRARMRKLRIGNPLDKSNDVGAIVDRVQLQRIRQMVESGRAD 362 Query: 362 GCSVWQSPDTTIPSGGCFFPPTLVTGVAPASTLAQEEIFGPVLVTMSFRTPDEAIALANN 421 G S WQ+ PS G FF PT V A LAQEEIFGPV+++M FRT DEA+ALAN+ Sbjct: 363 GLSCWQTA-LDAPSSGHFFAPTFFEDVPAAHALAQEEIFGPVVISMGFRTLDEAVALANH 421 Query: 422 SRYGLAASVWSETIGRALDVAPRLASGVVWINATNLFDAAVGFGGYRESGYGREGGREGI 481 SRYGLAAS+WSE I L VA +LA+GVVW+N N+FDAA GFGGYRESG+GREGGREG+ Sbjct: 422 SRYGLAASLWSENIDVCLTVAAQLAAGVVWVNGANMFDAAAGFGGYRESGFGREGGREGM 481 Query: 482 YEYLKPRAWLKLAERRAAQDV-VRDAAALDP--LSNVTSIDRTAKLFIGGKQARPDSGYS 538 +EYL P+ WL + AQD V+ AA L P SIDR+AK +IGGKQ RPDSGYS Sbjct: 482 HEYLVPK-WLHAPGAQQAQDAPVQVAAHLAPTEAGAARSIDRSAKFYIGGKQVRPDSGYS 540 Query: 539 LPVLAPDGTPVGEVAAGNRKDIRNAVEAARAAQKWSQASTHNRAQVLFYLAENLAVRADE 598 V + G +G GNRKDIRNAVE AR A WSQAS H RAQVL+Y AENL RA Sbjct: 541 FGVRSGSGALLGHAGFGNRKDIRNAVETARKAGNWSQASGHARAQVLYYFAENLGARAQT 600 Query: 599 FVRQLVVRNGATEAAARAEVDASVQRLFTYAAWADKFDGAVHTPPLRGVALAMHEPLGVI 658 F+ L +G +EAAA + + + R+F YAA ADK DG+VH+ V LAM+EP GV+ Sbjct: 601 FIAHLQAIDGISEAAASQQFEQVLARVFHYAAMADKHDGSVHSTLTAHVTLAMNEPFGVV 660 Query: 659 GIACPDEAPLLGFVSLAAPALAMGNRVVVLPSEASPLTVTDFYQVAETSDVPGGVLNIVT 718 G+ P PLL +SLA P LA GNRVV++P + L D YQV +TSD+P GVLNIV Sbjct: 661 GVRSPAHTPLLAALSLALPLLATGNRVVLVPPPDASLMFADLYQVLDTSDMPAGVLNIVW 720 Query: 719 GERGALLPALVKHDDVDAVWCFGSAADSTLVERESVGNLKRTFVDYGRQFDWFDR-ASEG 777 G+ L L HDDVDA+W FG AA + V+ S GNLK T+V RQ DW R +G Sbjct: 721 GDSDELAEVLALHDDVDALWYFGPAAGAARVQAASAGNLKSTWVQ-RRQLDWTSREQGQG 779 Query: 778 RPFLRQAVQVKNIWIPYGD 796 F+R A QVKN+WIPYG+ Sbjct: 780 GEFMRHATQVKNVWIPYGE 798 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: 1712 Number of extensions: 73 Number of successful extensions: 7 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: 798 Length adjustment: 41 Effective length of query: 755 Effective length of database: 757 Effective search space: 571535 Effective search space used: 571535 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