Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate AZOBR_RS26825 AZOBR_RS26825 aldehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__azobra:AZOBR_RS26825 Length = 494 Score = 285 bits (728), Expect = 3e-81 Identities = 171/464 (36%), Positives = 242/464 (52%), Gaps = 9/464 (1%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 +P VIA + G +VDAAV AA AA +GAW R+S +R +L + ++ Sbjct: 37 NPATGDVIATAADGGERDVDAAVRAAVAA-QGAWARLSARERGRLLVECGRRLVGHAEEI 95 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 +TGK + V+ A + + + E P + + R P Sbjct: 96 GRLLALETGKAIRTESRVEASLVADTLTFYGGLASELKGE----TVPFHPKMLTFTQREP 151 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 +GVVG I PWN+PL LM K+ PAL GN V+VK +EE P A + +VMN +PPGV Sbjct: 152 IGVVGAIIPWNVPLYLMALKIAPALVAGNAVIVKSAEEAPLAALRVIQVMNQL-LPPGVL 210 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263 N++ G GP G L +HP V +TFTG TG+ I AAD PV+LELGGK+ IV Sbjct: 211 NILSGDGPGC-GAPLVTHPGVGKVTFTGSVETGKIISHLAADKLIPVTLELGGKSPMIVM 269 Query: 264 ADCDLDKAIEGTLRSC-FANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDL 322 D DLDKAI+G + F GQ C + R++V + D F+ +LK + M +G P D Sbjct: 270 GDADLDKAIDGAVAGMRFTRQGQSCTASSRIFVHESLHDAFIDKLKAKVDAMTMGDPLDE 329 Query: 323 ATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDD 382 AT +G +IS + E+V SY + E L G +VQP ++TGL +D Sbjct: 330 ATDIGTIISPQQFERVQSYIALGETTAGAIAHRCSALPTDERLARGLFVQPVLFTGLAND 389 Query: 383 SVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAW 442 +AREEIFGP V+ F E+ + AND+D+GLA IWT +L A ++ G Sbjct: 390 HRLAREEIFGPVTCVIAFRDYEDALAMANDSDFGLAATIWTRDLRTALDATRRLQAGFVQ 449 Query: 443 VNSWFLRDLRTAFGGSKQSGIGREGGVHS-LEFYTELKNVCIKL 485 VN + ++GG KQSG+G+E + + L+ +T K V I + Sbjct: 450 VNQNLVVQPGLSYGGFKQSGLGKEASLEAMLDHFTHKKTVIINM 493 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: 529 Number of extensions: 28 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: 494 Length adjustment: 34 Effective length of query: 451 Effective length of database: 460 Effective search space: 207460 Effective search space used: 207460 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