Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_200825325.1 BZY95_RS07130 aldehyde dehydrogenase family protein
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_002151265.1:WP_200825325.1 Length = 484 Score = 370 bits (950), Expect = e-107 Identities = 196/474 (41%), Positives = 284/474 (59%), Gaps = 10/474 (2%) Query: 10 KWI-KGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSIL 68 +W+ GSG + + NPAD+D +L + DD + AI A F W TP +R IL Sbjct: 14 QWVASGSGATFENRNPADQDDLLGLFQASGVDDARRAIAAADRAFTAWRETPISQRAKIL 73 Query: 69 LKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADP 128 +A + + + ++FA +T EEGK L +S EVTRS L+FY I+G+T P D Sbjct: 74 NRAADYLMENVEQFARELTREEGKLLANSRDEVTRSAQTLRFYAVEGQTITGETFPQDDA 133 Query: 129 NTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVL 188 ++T +EPLGV +ITPWNFP+SIP K+APAL GNT V KP++ PL+ +L E L Sbjct: 134 KMTVYTQREPLGVATIITPWNFPISIPARKIAPALITGNTVVFKPSSDAPLIGYRLAEAL 193 Query: 189 SKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQL 248 AG+P GV N + G S +G+ I ++ + A+SFTGST G+RI++ TR Q+ Sbjct: 194 HHAGVPAGVFNFITGAASAIGEEITANPVVKAISFTGSTAAGERIHRAAA---MATRTQM 250 Query: 249 ELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVK 308 ELGGKN L V + AD+ A +L V+GGF LTGQ+CT TSR++I + ++ RL+E+VK Sbjct: 251 ELGGKNPLIVLEDADIDTAVDLTVKGGFSLTGQACTGTSRVLIARSRKQEYLTRLVEQVK 310 Query: 309 KWRVGPG-TEDVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIP----GKGYFLEP 363 ++G G +E + +GP+ Q L Y+E G+ A +YGG + KG+++ P Sbjct: 311 TLKIGNGMSEGIQIGPLATRQQLDTVLGYVETGRK-EATHVYGGEHLTEGDYAKGFYVTP 369 Query: 364 TIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFV 423 IF VT +MR+ +EEIFGPV++V E ++AI N YG AG+V + I F Sbjct: 370 AIFSDVTQEMRIAREEIFGPVVAVIEVDGYEDAIAKANDTPYGLAAGLVTKNFDYIQRFP 429 Query: 424 SRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEG 477 ++AG +K+N+ T G + APFGG K S +T++E G L+F+ + KTVY G Sbjct: 430 LDIQAGTVKINRTTTGNLVNAPFGGLKQSSTSTFRESGRAGLDFFTQTKTVYLG 483 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: 620 Number of extensions: 27 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: 484 Length adjustment: 34 Effective length of query: 444 Effective length of database: 450 Effective search space: 199800 Effective search space used: 199800 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 Apr 09 2024. 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