Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Ac3H11_4805 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= BRENDA::Q1XGK8 (486 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4805 Length = 491 Score = 323 bits (827), Expect = 1e-92 Identities = 191/479 (39%), Positives = 263/479 (54%), Gaps = 16/479 (3%) Query: 6 HFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGKLSVAE 65 H+I+G V AS F+ +P + ++G + E A VDAAV AA A W L+ AE Sbjct: 17 HYIDGQRV--ASDMRFDLHSPIDQALLGRISEGSPAHVDAAVSAAARAFPA-WSALTAAE 73 Query: 66 RAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVANEA 125 R L R A I R + F E D G S H +PR N FA+ ++ + Sbjct: 74 RKPYLDRFAAEIGKRAEAFCTLESNDAGVLLSRMKHGVVPRAMLNITWFAEHALSLQDRP 133 Query: 126 FEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEETPL 185 E A + P GV+ +I+PWN PL+L TWK+GPALA GN V+VKP E PL Sbjct: 134 IETEQ-----ATHLVRHDPAGVVAIITPWNAPLMLATWKLGPALAAGNCVIVKPPEWAPL 188 Query: 186 TATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRAAA 245 T++LL + AAG+P GV+N+V G G S GA L P + +FTG T + I ++A Sbjct: 189 TSSLLADCAHAAGLPPGVFNIVQG-AGVSTGARLVSDPRLARISFTGSVPTAKWIAQSAG 247 Query: 246 KGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDEFV 305 + SLELGGK+A IV D D+D A T + N GQVCL R V R + D FV Sbjct: 248 ANLVPCSLELGGKSAFIVLEDADIDNA-AATGALMYRNAGQVCLAGTRFLVHRKVHDAFV 306 Query: 306 ARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPDMPAH 365 A L+ E L +G P D ++ GP++ + E+V + Q+AV DG +++ GG H Sbjct: 307 AALRGYVEKLTVGDPRDGATEVGPIIHPRQVERVHGFVQRAVADGATLLWGGA-----QH 361 Query: 366 LAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAIWTE 425 G + QPT+ T + DS +V E+FGP ++ FD++EEAI LAN YGL + Sbjct: 362 PFGAQYYQPTLLTDVRQDSEIVQNEVFGPVLTLQTFDSDEEAIALANGTDYGLGGVCYGA 421 Query: 426 NGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNICV 484 A VA Q+ G +WVNS+ +RDL FGG K+SG+GREGG S EF+ ++K++ V Sbjct: 422 T-EHASAVAQQVRTGFIWVNSFGIRDLAAPFGGIKRSGVGREGGDWSFEFFCDVKDVVV 479 Lambda K H 0.318 0.136 0.411 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: 662 Number of extensions: 33 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: 486 Length of database: 491 Length adjustment: 34 Effective length of query: 452 Effective length of database: 457 Effective search space: 206564 Effective search space used: 206564 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