Align Aldehyde dehydrogenase; NAD/NADP-dependent aldehyde dehydrogenase; EC 1.2.1.3; EC 1.2.1.4 (characterized)
to candidate 200843 SO1678 methylmalonate-semialdehyde dehydrogenase (NCBI ptt file)
Query= SwissProt::Q8GAK7 (458 letters) >FitnessBrowser__MR1:200843 Length = 499 Score = 181 bits (459), Expect = 5e-50 Identities = 140/468 (29%), Positives = 219/468 (46%), Gaps = 27/468 (5%) Query: 3 IATIDPTTGITLKTFDAHTPEEVENRIARAEAAFRSLQNTSFEERARWMHKAADILESEA 62 I +P T+ ++ T +EV IA A+AAF++ + ERAR M + +L+ Sbjct: 22 IVVTNPANNATIAVINSATADEVHAAIASAKAAFKTWKEVPVSERARVMLRYQHLLKEHH 81 Query: 63 DEVARLIATEMGKTLTTAKYEALKSATGMRHFADHAQRYLSPETPVPASEVNASNLHVQF 122 DE+A ++A E GKT AK + + H + A + A ++ + Sbjct: 82 DELATILAHETGKTFEDAKGDVWRGIEVAEHACNIASLLMGETVENVARSIDT---YSYT 138 Query: 123 DPLGVVLAVMPWNYPLWQAVRFAAPALMAGNTGLLKHASNVPQCALYLGDLFARGGFPEG 182 PLGV + P+N+P + A+ GNT +LK + P L +LF G P+G Sbjct: 139 QPLGVCAGITPFNFPAMIPLWMFPLAIACGNTFILKPSEQDPMTPQRLVELFVEAGAPKG 198 Query: 183 AFQTLLVEGKDVIPLVDDARIRAVTLTGSVAAGSAIAEAAGRNIKRSVLELGGMDVFIVM 242 Q + + V L+ D ++A++ GSVA G I + N+KR G + ++M Sbjct: 199 VLQLIHGDKTAVDILLADPAVKAISFVGSVAVGQYIYKTGTDNLKRVQAFAGAKNHCVIM 258 Query: 243 PSADIEKAAAQAVIARLQNSGQSCIAAKRFYVHEDVYDRFEHLFVTGMAEAVA----GDP 298 P A+ ++ V A + +GQ C+A + V+ ++ + EA+A G Sbjct: 259 PDANKQQVINNLVGASVGAAGQRCMA-----ISVAVFVGAAKEWIPELKEALAKVRPGLW 313 Query: 299 LDESTSFGPLATERGRQDVHELVRDAREKGAAVQC---GGEIP----EGEGWYYPATVLT 351 D+ +GPL + + V +L+ +E+GA QC G + E W P T+ T Sbjct: 314 DDKDAGYGPLISPAAKVRVLKLIAQGKEEGA--QCLLDGSDFTVAGFESGNWVGP-TMFT 370 Query: 352 GVTEDMRIYREECFGPVACLYKVSSLQEAIALSNDSDFGLSSSVWTNDETEATEAARSIE 411 VT DM IY+EE FGPV C + SL++AI L N S +G +S++T A + IE Sbjct: 371 KVTTDMSIYKEEIFGPVLCCMESDSLEDAIELVNASPYGNGTSIFTASGAAARKYQHEIE 430 Query: 412 AGGVFIN-GLTASFPAVPFGGLKDSGYGRELSAYG---IREFVNIKTV 455 G V IN + P F G K S YG + AYG +R + KT+ Sbjct: 431 VGQVGINVPIPVPLPFFSFTGWKGSFYG-DQHAYGKQAVRFYTETKTI 477 Lambda K H 0.317 0.132 0.386 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: 491 Number of extensions: 26 Number of successful extensions: 4 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: 458 Length of database: 499 Length adjustment: 34 Effective length of query: 424 Effective length of database: 465 Effective search space: 197160 Effective search space used: 197160 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 (21.7 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