Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate 8501918 DvMF_2633 Aldehyde Dehydrogenase (RefSeq)
Query= curated2:P39616 (456 letters) >FitnessBrowser__Miya:8501918 Length = 460 Score = 248 bits (633), Expect = 3e-70 Identities = 146/458 (31%), Positives = 238/458 (51%), Gaps = 7/458 (1%) Query: 6 SIISKHKAYFAAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYSTEIG 65 ++ ++ KA+ A+G P +R++ LR+L++ V+ + L A+ D + E E+ Sbjct: 3 ALAARQKAFIASGAVLPSGARVDALRRLREGVQGYRDRLADAIRADYGRPEHPFLVREVV 62 Query: 66 IVLEEISFVMKRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLALSPL 125 VL EI +++K + + +RV L ++S + +P G V+ A W P + L PL Sbjct: 63 PVLHEIDWLIKAVPGFCGGRRVLPSLGQFKARSYVRRQPLGRVVAYAHWADPFRSLLVPL 122 Query: 126 IGAIAAGNTVVLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPFDYIF 185 AI AGN VVL+PS PA + ++++++ F ++VA+ GG + ALL D+++ Sbjct: 123 ADAIGAGNAVVLRPSAEAPATAEMVTRMVRQYFEPEHVAVVGGGAETDEALLATAPDFVW 182 Query: 186 FTGSVAVGKIVMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAGQTCI 245 + G + + AA L P GG S +VH DAD+ +AA+RIV+ KF +AGQ Sbjct: 183 YDGDARGARTIAVLAAPTLTPYAAITGGPSAALVHGDADMAMAARRIVWAKFLHAGQLRA 242 Query: 246 APDYLFVHEDIKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDGIPLT 305 APD L V + ++ + ++ + +GPQP + +G++VS + R L G L Sbjct: 243 APDVLLVQRTVLDRVLDALRTELERAFGPQPRTSADFGRMVSAAGFARQAERLAIGRALP 302 Query: 306 GGQSDPNHHK------IAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRP 359 G D + + PT+L V DDSPV++EE FGP+L + Y + E + P Sbjct: 303 FGPGDAANQPDRASLYVPPTLLTDVPDDSPVLREEGFGPVLVVRPYTRLDEATAFLAGLP 362 Query: 360 KPLALYLFTTNKEIERAVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSF 419 ALY FTT ++ N G +ND H+A P LP GGVGE+G G+ G Sbjct: 363 ALTALYAFTTAHARGERLMENTRAGAVLINDAATHLANPRLPQGGVGETGHGAMAGPAGL 422 Query: 420 NTFTHKKSVVKQTNRFDFAFRY-PSSKNGLRMIRKILK 456 TF+ ++ +N FD R+ P S L++++++ K Sbjct: 423 ATFSAPRATAVGSNFFDIPLRFAPGSDLKLKVLKRLYK 460 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: 474 Number of extensions: 16 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: 460 Length adjustment: 33 Effective length of query: 423 Effective length of database: 427 Effective search space: 180621 Effective search space used: 180621 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 17 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