Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_023431853.1 N177_RS08305 aldehyde dehydrogenase family protein
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_000496075.1:WP_023431853.1 Length = 484 Score = 490 bits (1261), Expect = e-143 Identities = 238/477 (49%), Positives = 326/477 (68%), Gaps = 1/477 (0%) Query: 16 LQGTKKLYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEW 75 L TK L+IDG+F SG +F T NPATG + + EA A DVD+AV++AR AF+ G W Sbjct: 6 LDVTKGLFIDGRFSAPLSGRSFATSNPATGSLITHVGEADAVDVDRAVRSARAAFE-GPW 64 Query: 76 RTMSPASRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWC 135 M A R RL+ +LA+L+ E+ EL LE+LD+GKP++ D+P ++ + YYAGW Sbjct: 65 GHMRAAERGRLLSRLAELVGENLDELVDLESLDSGKPVSAIRRQDLPAVLDTLTYYAGWA 124 Query: 136 TKITGQTIPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQ 195 KI GQ IP YT EP+GVVG I+PWNFPL++ +WK+ ALA GCT+VLKPAE Sbjct: 125 DKINGQVIPARADALTYTVREPIGVVGAIVPWNFPLMIGVWKLAPALACGCTVVLKPAEL 184 Query: 196 TPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMST 255 T L+AL L EL +AGFPAGV+N++PG G+ AG AL +H VDK+ FTGS +G++I+ + Sbjct: 185 TSLTALRLGELAMEAGFPAGVLNVVPGLGKTAGAALVDHPDVDKVTFTGSPAVGRQILRS 244 Query: 256 AAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDE 315 AA ++KRVTLELGGKS N++ PDA+++ A A G+ FN GQVC AGSRV +H+D +DE Sbjct: 245 AAGNLKRVTLELGGKSANVIFPDADVEAAAKAAAAGIFFNSGQVCSAGSRVLVHEDVHDE 304 Query: 316 VVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCPFEA 375 VV+ + A LR G L TQ+GPLVS+ Q ERVL Y++ G+ EGA GG + Sbjct: 305 VVERLVDRAARLRLGDPLDPATQMGPLVSETQMERVLGYVEIGRREGATVAVGGGRVGDE 364 Query: 376 GYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVK 435 G FVAPTV VE +M +++EEIFGPV++ + + +E + AN + Y LAAG+W+ ++ Sbjct: 365 GCFVAPTVLTGVEHDMRVSQEEIFGPVVSVVRFRDEEEAVRMANGTAYSLAAGVWSSDLG 424 Query: 436 QAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNYTEVKSVWVN 492 + H +A R++AGTVWVN + D P+GG + SG GRE G A++N+TE K+VW+N Sbjct: 425 RIHRLAKRIRAGTVWVNTFGPTDIRLPWGGSRDSGFGREHGEAAIENFTEPKAVWIN 481 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: 632 Number of extensions: 28 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: 495 Length of database: 484 Length adjustment: 34 Effective length of query: 461 Effective length of database: 450 Effective search space: 207450 Effective search space used: 207450 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