Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_057507564.1 ABB28_RS04920 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_001431535.1:WP_057507564.1 Length = 501 Score = 240 bits (613), Expect = 7e-68 Identities = 157/478 (32%), Positives = 252/478 (52%), Gaps = 15/478 (3%) Query: 21 KLYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSP 80 +L IDG+F+ S++ D NPAT + L + A ++VD AV AA++AF WR Sbjct: 9 RLLIDGQFIESSTAHWQDVVNPATQDVLAQVPFATTSEVDDAVAAAKEAFKT--WRKTPI 66 Query: 81 ASRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITG 140 +R+R+ K L+ E+ +ELA + + GK + + GD+ +E + + A G Sbjct: 67 GTRARIFLKYQQLIRENMSELAHTLSAEQGKTVPDA-EGDVFRGLEVVEHAAAIGNLQLG 125 Query: 141 QTIP-VSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLS 199 + V+ YT +P+GV I P+NFP ++ +W A+ATG T VLKP+EQ P+ Sbjct: 126 ELANNVANGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 185 Query: 200 ALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKS 259 + L EL +AG P GV+N++ G GE+ A+ +H + ++F GST +G + + A+ + Sbjct: 186 TMRLVELALEAGIPKGVLNVVHG-GEEVVNAICDHPDIKAVSFVGSTRVGTHVYNRASLA 244 Query: 260 IKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDE 319 KRV +G K+ ++LPDAN ++ + + GQ C A S + + + V D Sbjct: 245 GKRVQCMMGAKNHAVVLPDANKEQTLNAMVGAAFGAAGQRCMAASTLVLVGEARSWVPDL 304 Query: 320 MASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCP----FEA 375 +A A++L+ AG T +GP++S ERV I G ++GA G P FE Sbjct: 305 VAK-AKTLKVSAGSVAGTDVGPVISCSARERVEGLIASGLEQGATLDLDGRNPQVDGFEK 363 Query: 376 GYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVK 435 G FV PT+F+ V +M I +EEIFGPVL + ET+++ I N + G ++T++ Sbjct: 364 GNFVGPTIFSGVTTDMRIYQEEIFGPVLVILEAETLEDAIALVNSNPNGNGTAVFTQSGA 423 Query: 436 QAHYIADRLQAGTVWVNC-YNVFDAASPFGGYKQSGLGREMGSY---ALDNYTEVKSV 489 A + + G V +N V F G + S LG ++G Y + YT+ K++ Sbjct: 424 AARKFQEDIDVGQVGINVPIPVPVPLFSFTGSRASKLG-DLGPYGKQVVMFYTQTKTI 480 Lambda K H 0.316 0.133 0.391 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: 25 Number of successful extensions: 6 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: 495 Length of database: 501 Length adjustment: 34 Effective length of query: 461 Effective length of database: 467 Effective search space: 215287 Effective search space used: 215287 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 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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