Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_059151353.1 V474_RS10060 aldehyde dehydrogenase family protein
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_001046635.1:WP_059151353.1 Length = 501 Score = 451 bits (1159), Expect = e-131 Identities = 231/475 (48%), Positives = 314/475 (66%), Gaps = 9/475 (1%) Query: 22 LYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPA 81 L I G++ +A+G TF T +PATG L + +A AADVD AV AAR A W PA Sbjct: 25 LLIGGEWAQAANGGTFATLDPATGSELGQVAKAGAADVDAAVSAARAAL--AVWGATVPA 82 Query: 82 SRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITGQ 141 R+R+++K+ADL+E + +LA+LETLD GKP+ +IP A+ R++AG I G Sbjct: 83 ERARILWKVADLIEANIDDLAELETLDQGKPLFVGRWAEIPGAVSQFRFFAGQAMAIEGS 142 Query: 142 TI-------PVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAE 194 T+ P +T EPVGVV I+PWN PL++ K+ ALA GCT+VLKPAE Sbjct: 143 TLESSINYQPAGKQMRTWTVREPVGVVAAIVPWNSPLVLTAMKLAPALAAGCTVVLKPAE 202 Query: 195 QTPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMS 254 T L+AL L EL+ +AG PAGVINI+ G G + G AL H V KIAFTGST G+ ++ Sbjct: 203 DTSLTALRLGELMIEAGVPAGVINIVTGLGGETGAALAAHPGVAKIAFTGSTATGRAVLD 262 Query: 255 TAAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYD 314 A + KRVTLELGGKSP+I++PDA+L +AIPG N + FN GQVC AGSR+++H+ +D Sbjct: 263 AAKTNFKRVTLELGGKSPSIIMPDADLSQAIPGVANAIYFNGGQVCIAGSRLYVHRSVHD 322 Query: 315 EVVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCPFE 374 +VV+ +A YA+ L+ G GL DTQ+GP+VS ERV ++Q+ + EGA + GG E Sbjct: 323 QVVEGVAEYAKGLKLGHGLAADTQMGPVVSLRHAERVEGFLQRARAEGATMLAGGERTGE 382 Query: 375 AGYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENV 434 AG F+ PT+ +V+ M I +EE+FGPVL A ++ V+EVI AN SEYGLAA +WTE + Sbjct: 383 AGTFITPTLVVDVKPGMEIVREEVFGPVLVAQAFDDVEEVIAAANDSEYGLAASVWTEGL 442 Query: 435 KQAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNYTEVKSV 489 AH ++ ++AGTVW+NC+ ++D GG KQSG GR+ G AL+NY E K++ Sbjct: 443 SNAHRMSSAIKAGTVWINCHAMYDPTLAIGGVKQSGWGRDSGRQALENYLEWKTI 497 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: 646 Number of extensions: 21 Number of successful extensions: 3 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 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