Align Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= curated2:Q49Z69 (475 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 349 bits (895), Expect = e-100 Identities = 195/471 (41%), Positives = 271/471 (57%), Gaps = 2/471 (0%) Query: 1 MRNFTKQYINGEWVESTSGETLEVINPATEEVAGTIAKGNKEDVEKAVEAADNVYLEFRH 60 M+ ++ YI G+WV ++V NPATE V + +G D ++A AA + + Sbjct: 1 MQQHSRFYIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAA 60 Query: 61 TSVKERQDLLDQIVQEYKNRKEDLIQAITDELGAPLSVAENVHYQMGLDHFEA-ARDALN 119 S ER L +I K R+++L + I E+G P+ +A V + F A AR A Sbjct: 61 LSGAERGAFLQKIADGLKARQDELGRLIASEVGMPVKLATRVQAGNPIFTFAACARIAAE 120 Query: 120 DFQFEERRGDDLVVKEAIGVSGLITPWNFPTNQTSLKLAAAFAAGSPVVFKPSEETPFAA 179 F EER G LV+K G ITPWNFP +Q + K+ AA AAG VV KPSE P A Sbjct: 121 GFA-EERIGQSLVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNA 179 Query: 180 IILAEIFDKVGVPKGVFNLVNGDGQGVGNPLSEHPKVRMMSFTGSGPTGSSIMKKAAEDF 239 +LAE+ + G+P GVFNLV G G VG L+ HP + +SFTGS G + AA Sbjct: 180 FLLAEVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATV 239 Query: 240 KKVSLELGGKSPYIILDDADIDGAASAAANKVVFNTGQVCTAGTRTIVPASIKEDFLTAV 299 K+VSLELGGKS ++L DAD+ A N+GQ C+A TR +VP + Sbjct: 240 KRVSLELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALA 299 Query: 300 KEKFSQVKVGNPREEGTQVGPIISKKQFDQVQAYIDKGIEEGAELLYGGPGKPEGLDKGY 359 + + +G+P EG+++GP++S Q +V+A I++ + +GAELL GG PEGL GY Sbjct: 300 VQAAAAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGY 359 Query: 360 FARPTIFNNVDNSMTIAQEEIFGPVMSVITYNDLDEAIKIANDTKYGLAGYVYGSDKDTL 419 + RPT+F V +A+EE+FGPV++++TY D EA IAN T YGLA V+ +++ Sbjct: 360 YVRPTVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARA 419 Query: 420 HKVARSIEAGTVEINEAGRKPDLPFGGYKQSGLGREWGDYGIEEFLEVKSI 470 AR + AG V+IN A PFGG+KQSG GRE G +G+E+FLE +SI Sbjct: 420 LAFARRLRAGQVDINGAFFNLLAPFGGFKQSGYGRELGRHGVEDFLETQSI 470 Lambda K H 0.313 0.134 0.380 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: 539 Number of extensions: 16 Number of successful extensions: 1 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: 475 Length of database: 476 Length adjustment: 33 Effective length of query: 442 Effective length of database: 443 Effective search space: 195806 Effective search space used: 195806 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 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