Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate WP_047005389.1 AAW01_RS00220 coniferyl aldehyde dehydrogenase
Query= curated2:P39616 (456 letters) >NCBI__GCF_001010925.1:WP_047005389.1 Length = 483 Score = 322 bits (826), Expect = 1e-92 Identities = 183/440 (41%), Positives = 251/440 (57%), Gaps = 10/440 (2%) Query: 1 MNSIPSIISKHKAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDL-HKSEQEA 59 M + S+++ KA FAA E RL+ L +L+ + + L A+ D +S E Sbjct: 13 MPDLDSLLAAQKAAFAADRMPSREVRLDRLDRLQNLLLDNRQALADAISADFCGRSPVET 72 Query: 60 YSTEIGIVLEEISFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQ 119 EI +LE I + KRL+K KP++ LT + +++ + +P G V ++ PWN+P+ Sbjct: 73 DLAEIIPLLEGIKYYRKRLKKLMKPEKRHASLTVMPARAEVRYQPKGVVGIVVPWNFPVF 132 Query: 120 LALSPLIGAIAAGNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQ 179 LALSPLIG +AAGN +LK SE+TP +L L++ F D V + G +V+TA + Sbjct: 133 LALSPLIGVLAAGNRAMLKMSEFTPRTGELLGGLLAEKFSDDEVVLVNGDVEVATAFTKL 192 Query: 180 PFDYIFFTGSVAVGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTN 239 PFD++ FTGS AVG+ VM AAA+ L+PVTLELGGKSP I+H D ++ AAKRI FGK N Sbjct: 193 PFDHLVFTGSTAVGRKVMAAAAENLVPVTLELGGKSPAIIHPDFPMEEAAKRIAFGKVIN 252 Query: 240 AGQTCIAPDYLFVHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLN 299 AGQ CIAPDY+ + +RE Y P NP Y I++E RL +L Sbjct: 253 AGQICIAPDYILCPRSQVDAFADAFANEVRENY-PTYRDNPDYTAIITEAQRDRLTDWLA 311 Query: 300 DG-------IPLTGGQSD-PNHHKIAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEV 351 D + + D K+ TI V DD +MQ+EIFGPILP+ Y + E Sbjct: 312 DAEAKGARLMRVNPADEDLSGTRKLPVTIALDVSDDMTIMQDEIFGPILPIVPYDTLDEA 371 Query: 352 IEKVQSRPKPLALYLFTTNKEIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIG 411 + V R +PLALY F +K VL GG C+NDTL HV LPFGG+G SGIG Sbjct: 372 LAYVNERERPLALYYFDWDKSRADRVLARTHSGGACINDTLSHVTCDDLPFGGIGPSGIG 431 Query: 412 SYHGFDSFNTFTHKKSVVKQ 431 YHG + + TF+H K+VV++ Sbjct: 432 HYHGEEGYRTFSHAKAVVRK 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: 541 Number of extensions: 22 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: 483 Length adjustment: 33 Effective length of query: 423 Effective length of database: 450 Effective search space: 190350 Effective search space used: 190350 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