Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__PS:Dsui_0105 Length = 476 Score = 279 bits (713), Expect = 2e-79 Identities = 170/458 (37%), Positives = 243/458 (53%), Gaps = 13/458 (2%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 +P VIA+V E + D A AA AA AW +S A+R L +ADG+ R D+ Sbjct: 26 NPATETVIARVPEGTATDADRAARAAAAAFP-AWAALSGAERGAFLQKIADGLKARQDEL 84 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 + G P+ LA V F A + E + +G + ++ P Sbjct: 85 GRLIASEVGMPVKLATRVQAGNPIFTFAACARIAAEGFAE-------ERIGQ-SLVLKVP 136 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 G V I PWN PL + KVG ALA G TVV+KPSE P A LL EV+ AG+P GV+ Sbjct: 137 TGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAFLLAEVIEAAGLPAGVF 196 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263 N+V G+GP GE L +HP + A++FTG T G+ + AA + VSLELGGK+A++V Sbjct: 197 NLVTGYGP-VVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVKRVSLELGGKSASVVL 255 Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323 D DL A++GT+ CF N GQ C R+ V + + + + A LG P Sbjct: 256 PDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAVQAAAAYTLGDPLAEG 315 Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383 + +GPL+S R++V + ++AV GA ++ GG PE L G +V+PT++ + D+ Sbjct: 316 SRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSA--APEGLPTGYYVRPTVFGRVRPDA 373 Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443 +AREE+FGP ++ + E E AN DYGLA +W+ +RA A + G + Sbjct: 374 ALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARALAFARRLRAGQVDI 433 Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNV 481 N F +L FGG KQSG GRE G H +E + E +++ Sbjct: 434 NGAFF-NLLAPFGGFKQSGYGRELGRHGVEDFLETQSI 470 Lambda K H 0.318 0.135 0.406 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: 553 Number of extensions: 37 Number of successful extensions: 5 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: 485 Length of database: 476 Length adjustment: 34 Effective length of query: 451 Effective length of database: 442 Effective search space: 199342 Effective search space used: 199342 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 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