Align aldehyde dehydrogenase ALDH; EC 1.2.1.3 (characterized)
to candidate WP_040639379.1 MICLODRAFT_RS25285 aldehyde dehydrogenase family protein
Query= CharProtDB::CH_007936 (497 letters) >NCBI__GCF_000262405.1:WP_040639379.1 Length = 478 Score = 339 bits (869), Expect = 1e-97 Identities = 188/461 (40%), Positives = 266/461 (57%), Gaps = 8/461 (1%) Query: 32 EGKTFQVINPSNEKVITSVHEATEKDVDVAVAAARAAFEGPWRQVTPSERGILINKLADL 91 +G T V++P + ++ + T +D+D AV AARAAFEG W ++T +ERG L+ KLA Sbjct: 16 DGMTLDVLSPVDGSLLARIAAGTTQDIDEAVKAARAAFEGAWGELTATERGRLLMKLATA 75 Query: 92 MERDIDTLAAIESLDNGKAFTMAKVDLANSIGCLRYYAGWADKIHGQTIDTNPETLTYTR 151 +E D LA +ES DNGK ++ D +Y ADK+HG I Sbjct: 76 VEARADELAILESRDNGKPLRQSRADAIALARYFEFYGSAADKLHGDVIPYLNTHFIGVE 135 Query: 152 HEPVGVCGQIIPWNFPLLMWSWKIGPAVAAGNTVVLKTAEQTPLSALYAAKLIKEAGFPA 211 P GV G I+PWN+P+ ++ +G A+AAGN V+K AE L+ L + L +E GFP Sbjct: 136 RVPHGVTGHIVPWNYPMQIFGRSVGAALAAGNATVVKPAEDASLTILRVSALAREVGFPD 195 Query: 212 GVINVISGFGRTAGAAISSHMDIDKVAFTGSTLVGRTILQAAAKSNLKKVTLELGGKSPN 271 G +NV++G GRTAGAA+++H ID ++FTGS G T +Q AA N VTLELGGKS Sbjct: 196 GALNVVTGLGRTAGAALAAHSGIDFLSFTGSPETG-TAVQTAAARNHVGVTLELGGKSAQ 254 Query: 272 IVFDDADIDNAISWANFGIFFNHGQCCCAGSRILVQEGIYDKFVARFKERAQKNKVGNPF 331 +VFDDAD++ A+ I N GQ C AGSR+L+Q GI+ V ER + + G+P Sbjct: 255 VVFDDADLERALPTLVNAIIQNGGQTCSAGSRLLIQRGIFQDVVDAVAERFRTLRAGHP- 313 Query: 332 EQDTFQGPQVSQLQFDRIMEYINHGKKAGATVATGG----DRHGNEGYFIQPTVFTDVTS 387 E + GP ++Q Q R++ Y+ G+ G V G D GY++ P V Sbjct: 314 EHEPDLGPMINQAQQRRVLGYLERGRNEGLNVVGEGVVALDAPAG-GYYVAPAFLAPVPH 372 Query: 388 DMKIAQEEIFGPVVTIQKFKDEAEAIKIGNSTDYGLAAAVHTKNVNTAIRVSNALKAGTV 447 + ++QEE+FGPV+ F DEAEA ++ N T YGLAA V T++ + RV+ +++AG V Sbjct: 373 ESILSQEEVFGPVLVATPFDDEAEATRLANGTPYGLAAGVWTRDAMRSTRVARSIRAGQV 432 Query: 448 WINNYNM-ISYQAPFGGFKQSGLGRELGSYALENYTQIKTV 487 ++N Y + PFGGF +SG GRE G L +T KT+ Sbjct: 433 FVNCYGAGGGIELPFGGFGRSGHGREKGFEGLVEFTTTKTL 473 Lambda K H 0.318 0.134 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: 518 Number of extensions: 26 Number of successful extensions: 5 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: 497 Length of database: 478 Length adjustment: 34 Effective length of query: 463 Effective length of database: 444 Effective search space: 205572 Effective search space used: 205572 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: 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