Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_010531933.1 ON01_RS15200 aldehyde dehydrogenase family protein
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_000224785.1:WP_010531933.1 Length = 480 Score = 360 bits (924), Expect = e-104 Identities = 195/477 (40%), Positives = 284/477 (59%), Gaps = 8/477 (1%) Query: 39 IFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDA 98 ++IN +W D+ ++T NPSTGEV+ + G +DVDKAV+AA+ +F + WRR+ Sbjct: 6 MYINGKWEDSHDKETINVNNPSTGEVMTTIPRGKNDDVDKAVRAAKDSF-VSEEWRRVKP 64 Query: 99 SHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHG 158 RGR+L + ++ +R LA LET+D GKP Y D+D ++ +Y G ADK G Sbjct: 65 FERGRILCEVVAQLKENRDELARLETMDVGKPLTQGY-ADIDAAIRYFEFYGGAADKVMG 123 Query: 159 KTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTA 218 TIPI+ Y EP+GV I+PWN+P+ + + + A+A GN VV+K AE TPLTA Sbjct: 124 DTIPIEDGLIDYVIREPIGVTAHIVPWNYPIQILSRSVAAAIAMGNTVVVKSAEDTPLTA 183 Query: 219 LYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSN 278 +A + P GV N V G+G AGAA++SH ++ + FTGS G + AA +SN Sbjct: 184 AKIAEYFDQTDLPEGVFNHVTGYGYEAGAALSSHPLINHLTFTGSVGTGTAVANAA-TSN 242 Query: 279 LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338 + VTLELGGKSPNI+ SD D+D AVE A+ N GQ C AGSR ++E F+++ Sbjct: 243 VVPVTLELGGKSPNIVFSDCDVDKAVEGVVKAIIQNAGQTCSAGSRLLIEESFKQTFLDK 302 Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADR---G 395 V + K+ VG D GP +++ QF +IL +I+ +QEG L G + ++ Sbjct: 303 LVNKFKTLSVGPAIDDH-NLGPILNQKQFDRILEFISLAEQEGTVLTGGKRVKYEQYENA 361 Query: 396 YFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDK 455 +++PT+ ++ A+EEIFGPV+ + FK +E + AN++ YGL ++TKD++K Sbjct: 362 CYLEPTIIDNLSLNSKAAQEEIFGPVLSVFTFKNEQEAIDIANSTDYGLVTGIWTKDINK 421 Query: 456 ANYLSQALQAGTVWVNCYDVFGA-QSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVK 511 A+ L + +G V++N Y G Q PFGGYK SG GRE G L YT+VK V +K Sbjct: 422 AHLLMSRIDSGQVFINNYGAGGGIQMPFGGYKKSGFGREKGWIALYNYTQVKNVAIK 478 Lambda K H 0.319 0.136 0.409 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: 625 Number of extensions: 25 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: 517 Length of database: 480 Length adjustment: 34 Effective length of query: 483 Effective length of database: 446 Effective search space: 215418 Effective search space used: 215418 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: 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