Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Ac3H11_1486 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1486 Length = 485 Score = 350 bits (899), Expect = e-101 Identities = 194/469 (41%), Positives = 275/469 (58%), Gaps = 13/469 (2%) Query: 50 SRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLA 109 SR+ F TVNP+T EV+ +VA G +V AV AA+ AF W + A R +L+ +L Sbjct: 14 SREYFETVNPATQEVLAEVASGGAAEVHAAVAAAKDAFPA---WAGLPAPERAKLVRKLG 70 Query: 110 DLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFS 169 DLI + LA ET D G+ + + Y+A + G T P + Sbjct: 71 DLIAAEVPTLALTETKDTGQVIGQTGKALIPRAADNFYYFAEMCTRVDGHTYPTP-THLN 129 Query: 170 YTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAG 229 YT PVGVC I PWN P + WK+ PALA GN V+K++E +PLTA + L EAG Sbjct: 130 YTLFHPVGVCALISPWNVPFMTSTWKVAPALAFGNTAVLKMSELSPLTAARLGELALEAG 189 Query: 230 FPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELGGK 289 P GV+N+V G+G AG + +H DV ++FTGST G I AAG LK+ ++ELGGK Sbjct: 190 IPAGVLNVVHGYGKDAGEPLCTHPDVRAISFTGSTATGNRIVQAAG---LKKFSMELGGK 246 Query: 290 SPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVG 349 SP ++ +DAD+D A++ A F +F N G+ C AGSR VQ+ IY +F E+ ARA+ VVG Sbjct: 247 SPFVVFADADLDRALDAALFMIFSNNGERCTAGSRILVQKSIYADFAEKFAARARRIVVG 306 Query: 350 NPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD------RGYFIQPTVF 403 +P D KT GP + + K+ YI G +EGA LLCGG D +G F+ PTVF Sbjct: 307 DPLDEKTIVGPMISQAHLAKVRSYIELGPKEGATLLCGGLGTPDLPAHLQKGNFVLPTVF 366 Query: 404 GDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQAL 463 DV + M IA+EEIFGPV ++ F+ E + AN+ YGL++ V+T+++ +A+ ++ + Sbjct: 367 ADVDNRMKIAQEEIFGPVACLIPFEDEAEAIRLANDIQYGLSSYVWTENIGRAHRVAAGI 426 Query: 464 QAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512 +AG +VN +V + PFGG K SG+GRE G + + + E K + V + Sbjct: 427 EAGMCFVNSQNVRDLRQPFGGTKGSGTGREGGTWSYEVFLEPKNIAVSM 475 Lambda K H 0.319 0.136 0.409 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: 36 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: 517 Length of database: 485 Length adjustment: 34 Effective length of query: 483 Effective length of database: 451 Effective search space: 217833 Effective search space used: 217833 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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