Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >NCBI__GCF_000009985.1:WP_011383248.1 Length = 485 Score = 347 bits (890), Expect = e-100 Identities = 194/469 (41%), Positives = 277/469 (59%), Gaps = 16/469 (3%) Query: 50 SRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLA 109 S T +NP+ EVICQ+A G + +V +AV AA+ AF W + AS R +LL ++ Sbjct: 13 SASTIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFP---KWAGLPASQRAKLLRKVG 69 Query: 110 DLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFS 169 DLI + +A LE+LD G+ Y + + + ++A G+T P + D + Sbjct: 70 DLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGETYPTN-DHLN 128 Query: 170 YTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAG 229 YT ++PVGV G I PWN P + WK P LA GN V+K++E +PL+A + LI EAG Sbjct: 129 YTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADRLGQLILEAG 188 Query: 230 FPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIG-RVIQVAAGSSNLKRVTLELGG 288 P GV NIV G+G G A+ H DV V+FTGST G R+IQ S LK+ ++ELGG Sbjct: 189 IPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQ----SGGLKKYSMELGG 244 Query: 289 KSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVV 348 KSPNII D D + AV+ A A++ N G+ C G+R VQ+ +YD FV R + VV Sbjct: 245 KSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALAERTRKVVV 304 Query: 349 GNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGG-----GIA--ADRGYFIQPT 401 G+P D T GP + +KK+ YI G EGA+++ GG G+A G F++PT Sbjct: 305 GDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHLKNGNFVRPT 364 Query: 402 VFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQ 461 V DV + +A+EEIFGPV +++FK E + AN ++YGLA+ V+T++ +A +++ Sbjct: 365 VLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTENGARAIRMAE 424 Query: 462 ALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTV 510 ++AG V+VN +V + PFGG K SG+GRE G Y +A+ EVK V V Sbjct: 425 GIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNVCV 473 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: 628 Number of extensions: 31 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