Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_043458449.1 H537_RS0109120 aldehyde dehydrogenase family protein
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_000430725.1:WP_043458449.1 Length = 483 Score = 357 bits (916), Expect = e-103 Identities = 193/480 (40%), Positives = 283/480 (58%), Gaps = 18/480 (3%) Query: 7 LADKWIKGS--GEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKR 64 + KWI+GS GE +INP+D V+ ++ +AI A A +W+ +R Sbjct: 8 IGGKWIEGSSAGE---NINPSDTRDVIGLYARASQAQALDAIGAAHAALPKWAAATPQQR 64 Query: 65 GSILLKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLP 124 +L G + E A L+ EEGK L D+ EVTR+ + KF+ A +I G+ L Sbjct: 65 ADVLDAVGSEVAARKAELADLLAREEGKALADATGEVTRAAQIFKFFAGEALRIPGELLA 124 Query: 125 SADPNTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKL 184 S P + +EP+GVV++ITPWNFP++IP WK+APALA GNT V KPA P L Sbjct: 125 STRPGMSVEITREPVGVVSIITPWNFPIAIPAWKIAPALAYGNTVVFKPAELVPGSAWAL 184 Query: 185 VEVLSKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRI-YKLVGNKNRM 243 E+LS+AGLP G NLV+G+G ++GDT++ D +AAV+FTGS G+++ V + M Sbjct: 185 AEILSRAGLPAGTFNLVMGRGRDIGDTLLQDPRVAAVTFTGSEATGRKVAATCVTRRGAM 244 Query: 244 TRIQLELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRL 303 + QLE+GGKN L V ADL +A AV G + TGQ CTA+SRL+++ ++ +F + Sbjct: 245 AKFQLEMGGKNPLVVLDDADLDVAVSCAVNGAYFGTGQRCTASSRLVVSAGIHDRFVAAM 304 Query: 304 LERVKKWRVG----PGTEDVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPG--- 356 ++R+ +VG PGT +GPVVD Q ++DL+YI G+ GA L +GG + Sbjct: 305 VDRLATLKVGDARNPGTV---IGPVVDAQQLRQDLDYIAIGREEGATLAFGGQALQSVDG 361 Query: 357 -KGYFLEPTIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASD 415 G++L+P +F G ++ MR+ +EEIFGPV SV +D DEA+ + N ++G +AG+ + Sbjct: 362 QPGHYLQPALFTGTSNAMRINREEIFGPVASVIRVRDADEALAVANDTEFGLSAGVCTTS 421 Query: 416 IKAINEFVSRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475 ++ F ++AG++ VN PT G++ PFGG K S +E G A EFY KT Y Sbjct: 422 LRMAAHFKRELQAGMVMVNAPTAGVDAHVPFGGRKGSSYGP-REQGRHAAEFYTSVKTTY 480 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: 606 Number of extensions: 21 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: 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