Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate WP_008990590.1 I215_RS03585 aldehyde dehydrogenase
Query= curated2:P39616 (456 letters) >NCBI__GCF_000300875.1:WP_008990590.1 Length = 455 Score = 402 bits (1032), Expect = e-116 Identities = 202/449 (44%), Positives = 287/449 (63%), Gaps = 2/449 (0%) Query: 4 IPSIISKHKAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYSTE 63 I ++I +F G T + +R +L+ LK + E ++ A+Y+DL K EA +TE Sbjct: 5 ISNLIKGQDVFFKGGGTLAISTRKQLLKALKDTIVNREEVILKAIYKDLKKPTFEALATE 64 Query: 64 IGIVLEEISFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLALS 123 I IV+ EI+ +K + KW++PKRV + + + S S I EPYG +L+I+PWNYP LA+ Sbjct: 65 INIVIGEINNTLKHIDKWTRPKRVASSILNFPSTSRIHQEPYGRILIISPWNYPFALAII 124 Query: 124 PLIGAIAAGNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPFDY 183 PLIGA+AAGNT+VLKPSE +P +AI+ ++I +F D+V++ G +S LL+ +DY Sbjct: 125 PLIGALAAGNTIVLKPSEMSPNTTAIIQEIIQDIFDQDHVSVVVGDKKISQRLLEFRWDY 184 Query: 184 IFFTGSVAVGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAGQT 243 IFFTGS VGK V AA+ L PVTLELGGKSPCIV A + AKRIV+GKF NAGQ+ Sbjct: 185 IFFTGSTEVGKYVYSKAAEHLTPVTLELGGKSPCIVDSTASFKHLAKRIVWGKFLNAGQS 244 Query: 244 CIAPDYLFVHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDGIP 303 CIAPDYL VH +K +L E+K I + Y Y I++ H QRLL + D Sbjct: 245 CIAPDYLLVHYKVKDRLINELKEEINKAYPDLCNSTSDYANIINTDHSQRLLKLIQDQEV 304 Query: 304 LTGGQSDPNHHKIAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRPKPLA 363 L GG D PT++ + DSP+MQ+EIFGPILP+ +++ ++ + + KPLA Sbjct: 305 LFGGTVD--GQLFVPTLVNEPHIDSPLMQQEIFGPILPIIGFQSFEQIQQIIDRFEKPLA 362 Query: 364 LYLFTTNKEIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSFNTFT 423 LY+F++ V+ + SFGGG +NDT++H A LPFGGVG SGIG+YHG +F TF+ Sbjct: 363 LYVFSSENSFTDKVIQSFSFGGGVINDTMVHYADKNLPFGGVGHSGIGAYHGDCTFKTFS 422 Query: 424 HKKSVVKQTNRFDFAFRYPSSKNGLRMIR 452 H+K++V++++ D RYP K L+ ++ Sbjct: 423 HQKAIVQRSSWLDIPLRYPPYKGKLKWLK 451 Lambda K H 0.320 0.137 0.401 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: 589 Number of extensions: 23 Number of successful extensions: 2 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: 456 Length of database: 455 Length adjustment: 33 Effective length of query: 423 Effective length of database: 422 Effective search space: 178506 Effective search space used: 178506 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: 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