Align Putative aldehyde dehydrogenase AldX; EC 1.2.1.3 (characterized)
to candidate WP_068862316.1 I603_RS03110 coniferyl aldehyde dehydrogenase
Query= SwissProt::P46329 (445 letters) >NCBI__GCF_001677335.1:WP_068862316.1 Length = 483 Score = 320 bits (820), Expect = 6e-92 Identities = 182/454 (40%), Positives = 259/454 (57%), Gaps = 18/454 (3%) Query: 1 MEQQVKDDIQRVFQLQKKQQKALRASTAEQRREKLQRFLDSVIAHEEEIIEAIRKDV-RK 59 M +D+++ + Q+ A R QR+++++R + V H EE +A+ D + Sbjct: 8 MADDRRDELEALLARQRAAFTASRPEPLSQRKDRIRRAMALVKEHGEEFAKAMSADFGSR 67 Query: 60 PYHEVKKAEIEGTKKAIRDNMNNLEQWMAP--KEVGSSLSP-DANGILMYEPKGVTLILG 116 + +I T A + +++QW P ++V L A + YEPKGV IL Sbjct: 68 SIQQSMLTDIAATVGAGAHALKHIDQWSKPEKRKVQFPLGLLGARAEVRYEPKGVIGILS 127 Query: 117 PWNYPFMLTMAPLAASLAAGNSAIVKLSDFTMNTSNIAAKVIRDAFDEKEVAIFEGEVEV 176 PWN+P L PL LAAGN A++K S+FT TS + A++ + F +EVA+ G EV Sbjct: 128 PWNFPVQLAYGPLMQVLAAGNRAMIKPSEFTERTSELMAQLTAEYFAPEEVAVMTGGPEV 187 Query: 177 ATELLDQPFDHIFFTGSTNVGKIVMTAAAKHLASVTLELGGKSPTIIDSEYDLMDAAKKI 236 A PFDH+ FTGST G+ VM AAA++L VTLELGGKSP I+ D A ++I Sbjct: 188 AAAFSSLPFDHLVFTGSTATGRRVMQAAAENLVPVTLELGGKSPVIMGRSADFAKAGERI 247 Query: 237 AVGKFVNAGQTCIAPDYLFIKKDVQDRFAGILQTVVNAGFMEDDHTPDRSKFTQIVNDRN 296 A+GK +NAGQ C+APDYL + D D + V A D + IV+DR+ Sbjct: 248 AIGKMMNAGQICLAPDYLMVPDDKADE---AVAGVTGAAAAMYPRLLDNDDYASIVSDRH 304 Query: 297 FNRVKDLFDDAIERGAEVV--------FGGVFDASDRTISPTVLKNVTPDMKIMQEEIFA 348 F R++ L DA ++GAEV+ FG +A+ R + TVL+ V +M +MQEEIF Sbjct: 305 FERLQGLVADARDKGAEVIEVNPAGEDFG---NANQRKMPLTVLRGVNDEMTVMQEEIFG 361 Query: 349 SILPMMNYEDIDEVIDYVNDRDKPLALYVFSKNQDLIDNVLQHTTSGNAAINDVVVHFSD 408 +LP+M Y+ +D+ +DYVND D+PL LY F +++ + VL T SG NDVV H S Sbjct: 362 PVLPVMTYKSVDQAVDYVNDHDRPLGLYYFGEDRAEQERVLTRTISGGVTTNDVVFHVSM 421 Query: 409 VNLPFGGVNTSGIGSYHGVYGFKEFSHEKGVFIQ 442 +LPFGGV SG+GSYH + GF+EFSH + V+ Q Sbjct: 422 EDLPFGGVGPSGMGSYHAIEGFREFSHARAVYHQ 455 Lambda K H 0.318 0.134 0.378 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: 521 Number of extensions: 29 Number of successful extensions: 3 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: 445 Length of database: 483 Length adjustment: 33 Effective length of query: 412 Effective length of database: 450 Effective search space: 185400 Effective search space used: 185400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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