Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate WP_109968015.1 DK846_RS05900 aldehyde dehydrogenase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_1229 (505 letters) >NCBI__GCF_003173355.1:WP_109968015.1 Length = 473 Score = 188 bits (477), Expect = 4e-52 Identities = 142/473 (30%), Positives = 223/473 (47%), Gaps = 18/473 (3%) Query: 21 VESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGARMRIMLKL 80 VE ++ + + +VNP + +V+ +V +A +++ A+ AA R ++ +L Sbjct: 11 VERRSEDRYLVVNPFSGEVVGQVSRCSAEDIEEALQAATAGSTVTAELAAHQRATVLRRL 70 Query: 81 QALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVV----EHACSIGSLQMGEFAENVA 136 L+ H + +L E GK +AEG+ R +E + E A IG ++ V Sbjct: 71 VDLMTAHREEFITLLIAEGGKPRRNAEGETARAIETILISAEEAVRIGG-EVIPLDRTVP 129 Query: 137 G-GVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTMLLVE 195 G G R P+GV GITPFNFP + A+A GN +LKP+ P+S++LL Sbjct: 130 GEGCIGIVQRFPVGVVLGITPFNFPLNLACHKLGPAVASGNAIILKPASATPLSSLLLGR 189 Query: 196 LAIEAGIPPGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKRVQSM 255 L +EAG PP ++V+ D + L + I SF GS VG H+ A +V Sbjct: 190 LLLEAGYPPAAVSVLICSPDDAERLAADQRIGCFSFTGSPEVGWHLRSRATY--AKVTLE 247 Query: 256 MGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATS-VVVLVGAAKQWLPDLKALAQK 314 +G +V D + A + ++ GF AGQ C++ V V + L L LA Sbjct: 248 LGGNGAVIVHEDCDLSHAASRIIEGGFSQAGQVCISVQRVFVHRPVFEPLLTRLGELADG 307 Query: 315 LKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGNFVGPT 374 L V S+P TDVG +ISK A L I+ GA L + G +S G+ + PT Sbjct: 308 LVVGDPSDPKTDVGSMISKEAAEHALKRIQDACSAGATL-IKGGSLS------GSLLQPT 360 Query: 375 LFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAARKFQT 434 + +G M++ +E+F P++ V DT +QA+A VN + +G G+FT+ R + Sbjct: 361 ILTGTKAGMEVNCREVFAPIITVTPYDTFEQAVADVNDSVYGLQAGVFTRDLLRVRYAFS 420 Query: 435 EIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTAR 487 + VG V I V + G + S G GP + ++ T T+ + R Sbjct: 421 HLKVGTVVIGDIPTFRVDMMPYGGVKRSGSGREGP--RYAIEEMTDTRMMIIR 471 Lambda K H 0.319 0.135 0.397 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: 515 Number of extensions: 23 Number of successful extensions: 4 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: 505 Length of database: 473 Length adjustment: 34 Effective length of query: 471 Effective length of database: 439 Effective search space: 206769 Effective search space used: 206769 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 (21.7 bits) S2: 52 (24.6 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