Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 7025959 Shewana3_3107 methylmalonate-semialdehyde dehydrogenase [acylating] (RefSeq)
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__ANA3:7025959 Length = 496 Score = 266 bits (680), Expect = 1e-75 Identities = 154/451 (34%), Positives = 241/451 (53%), Gaps = 8/451 (1%) Query: 33 KIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEFALLMTLEEGK 92 ++ L ++D+V AI A + FD WS+ R +L K L+EQ E A L+TLE GK Sbjct: 33 QVSLASRDEVSAAIAIAKSAFDTWSQVTPLNRARVLFKFKALVEQHMDELAQLITLEHGK 92 Query: 93 TLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGVVALITPWNFPL 152 L D+ E+ R +++F + + G+ ++V + LGVVA I P+NFP+ Sbjct: 93 VLDDARGELIRGLEVVEFACGIPHLLKGEHTEQVGGGVDAWSVNQALGVVAGIAPFNFPV 152 Query: 153 SIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLVVGKGSEVGDTI 212 +P+W A+A GNT ++KP+ K P V ++ E+L++AGLP GV N+V G E DT+ Sbjct: 153 MVPMWMFPIAIACGNTFIMKPSEKDPSAVMRIAELLTQAGLPAGVFNVVNG-DKEAVDTL 211 Query: 213 VSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSADLTLAAELAV 272 +S ++I AVSF GST + + IY + R+Q G KN + + ADL A + Sbjct: 212 LSHEDIQAVSFVGSTPIAEYIYSTASKHGK--RVQALGGAKNHMLLMPDADLDQAVSALM 269 Query: 273 RGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPG-TEDVDMGPVVDEGQFK 331 +G G+ C A S ++ DV + +LL ++++ +VG G T +++MGP++ Sbjct: 270 GAAYGSAGERCMAISVVLAVGDVGDKLVDKLLPQIQQLKVGNGLTPEMEMGPLISRQHLA 329 Query: 332 KDLEYIEYGKNVGAKLIYGGNIIP----GKGYFLEPTIFEGVTSDMRLFKEEIFGPVLSV 387 K E+++ G GA L+ G + +GYFL +F+ VT +MR+++EEIFGPVLS+ Sbjct: 330 KVTEFVDAGVKEGATLVVDGRQLTVADHQQGYFLGACLFDNVTPEMRIYREEIFGPVLSI 389 Query: 388 TEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVGLELQAPFG 447 KD A+ L+N ++G+ I +A F V+ G++ VN P FG Sbjct: 390 VRVKDYASALALINQHEFGNGTAIFTQSGEAARHFCHHVQVGMVGVNVPIPVPMAFHSFG 449 Query: 448 GFKNSGATTWKEMGEDALEFYLKEKTVYEGW 478 G+K S G D + FY K K + W Sbjct: 450 GWKRSLFGPLHMHGPDGVRFYTKRKAITARW 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: 566 Number of extensions: 37 Number of successful extensions: 7 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: 496 Length adjustment: 34 Effective length of query: 444 Effective length of database: 462 Effective search space: 205128 Effective search space used: 205128 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: 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