Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Ac3H11_4805 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4805 Length = 491 Score = 313 bits (801), Expect = 1e-89 Identities = 184/460 (40%), Positives = 254/460 (55%), Gaps = 14/460 (3%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 SP++ A++ ++ E A VDAAV+AA A AW ++ A+R L A I +R + F Sbjct: 34 SPIDQALLGRISEGSPAHVDAAVSAAARAFP-AWSALTAAERKPYLDRFAAEIGKRAEAF 92 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 E D G +S +H +PR N FA+ ++ E A + P Sbjct: 93 CTLESNDAGVLLSRMKHGVVPRAMLNITWFAEHALSLQDRPIETEQ-----ATHLVRHDP 147 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 GVV +I PWN PL+L TWK+GPALA GN V+VKP E P T++LL + + AG+PPGV+ Sbjct: 148 AGVVAIITPWNAPLMLATWKLGPALAAGNCVIVKPPEWAPLTSSLLADCAHAAGLPPGVF 207 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263 N+V G G STG L S P + I+FTG T + I ++A P SLELGGK+A IV Sbjct: 208 NIVQGAGV-STGARLVSDPRLARISFTGSVPTAKWIAQSAGANLVPCSLELGGKSAFIVL 266 Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323 D D+D A T + N GQVCL R V R + D FV+ L+ E + +G P D A Sbjct: 267 EDADIDNA-AATGALMYRNAGQVCLAGTRFLVHRKVHDAFVAALRGYVEKLTVGDPRDGA 325 Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383 T +GP+I E+V + ++AV GAT++ GG G + QPT+ T + DS Sbjct: 326 TEVGPIIHPRQVERVHGFVQRAVADGATLLWGGAQHPF-----GAQYYQPTLLTDVRQDS 380 Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443 + + E+FGP + FDS+EE I AN DYGL + A VA + G WV Sbjct: 381 EIVQNEVFGPVLTLQTFDSDEEAIALANGTDYGLGGVCYGAT-EHASAVAQQVRTGFIWV 439 Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCI 483 NS+ +RDL FGG K+SG+GREGG S EF+ ++K+V + Sbjct: 440 NSFGIRDLAAPFGGIKRSGVGREGGDWSFEFFCDVKDVVV 479 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: 566 Number of extensions: 19 Number of successful extensions: 6 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: 491 Length adjustment: 34 Effective length of query: 451 Effective length of database: 457 Effective search space: 206107 Effective search space used: 206107 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: 52 (24.6 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