Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_090272720.1 BLU11_RS07260 aldehyde dehydrogenase family protein
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_900105005.1:WP_090272720.1 Length = 483 Score = 335 bits (859), Expect = 2e-96 Identities = 183/457 (40%), Positives = 266/457 (58%), Gaps = 6/457 (1%) Query: 23 NPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEF 82 NP++ + ++ + ++AI A W RT R IL + G + + QE Sbjct: 28 NPSNAEEIVDRFARADAALTEKAIAAARDAAGSWGRTNPQVRADILDRIGSEILERRQEL 87 Query: 83 ALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGVV 142 A L++ EEGK +++++ EV R+ KFY + +G+ S + +P+GVV Sbjct: 88 AELLSREEGKVVREALGEVERAGRSFKFYAQEVLRANGEKYESVREGVSVDVFTQPIGVV 147 Query: 143 ALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLVV 202 +I+PWNFP++IP WK APALA GNT V+KPA P L E++S++G+P GV NLV+ Sbjct: 148 GIISPWNFPIAIPAWKAAPALAFGNTVVMKPAELVPSSAWALAEIISRSGMPAGVFNLVI 207 Query: 203 GKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSA 262 G G VGDTI+ + A++FTGS G+++ ++ R+ R+QLE+GGKN L V A Sbjct: 208 GPGRTVGDTIIRSPKVDAITFTGSEGTGRQVAEIAA--QRLIRVQLEMGGKNPLVVLDDA 265 Query: 263 DLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVG-PGTEDVDM 321 DL +A E+A+ G F TGQ CTA+SRLI+ ++ +F RL ER + RVG P D D+ Sbjct: 266 DLDVAIEVALNGSFYSTGQRCTASSRLIVTTGIHDEFVARLAERTRALRVGDPLCADTDI 325 Query: 322 GPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPG-KG-YFLEPTIFEGVTSDMRLFKEE 379 GPVVD Q K++L YIE G GA LI GG + KG Y P +F V MR+++EE Sbjct: 326 GPVVDPSQLKQNLAYIESGLQEGATLICGGEYLENDKGAYHFSPALFVDVQPHMRIYREE 385 Query: 380 IFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVG 439 IFGPVLSV + + +EA++ Y +AGIV + +K F AG++ VN PT G Sbjct: 386 IFGPVLSVLKVANYEEALQAAEDTQYSLSAGIVTTSLKYAEHFKKHSSAGMVMVNLPTAG 445 Query: 440 LELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYE 476 ++ APFGG + S +E G A +F+ + KT Y+ Sbjct: 446 VDYHAPFGGNRGSSLGP-REQGTYARQFFTRVKTAYQ 481 Lambda K H 0.316 0.135 0.389 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: 21 Number of successful extensions: 4 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: 478 Length of database: 483 Length adjustment: 34 Effective length of query: 444 Effective length of database: 449 Effective search space: 199356 Effective search space used: 199356 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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