Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_012173167.1 AZC_RS23810 acyl-CoA dehydrogenase family protein
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_000010525.1:WP_012173167.1 Length = 564 Score = 214 bits (544), Expect = 6e-60 Identities = 132/384 (34%), Positives = 207/384 (53%), Gaps = 15/384 (3%) Query: 5 DEQLQ-ISDAARQFAQERLKPFAAEWDREHRF-PKEAIGEMAELGFFGMLVPEQWGGCDT 62 DE L+ + R+F + + P A EW ++ + P E IG +AELG FG+ +PE++GG Sbjct: 177 DETLEAMRSEIRRFVEAEVVPHAHEWHLKNAYIPLEVIGRLAELGVFGLTIPEEYGGLGL 236 Query: 63 GYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFA 122 A + EE++ G ++ + + I+ G D+QK +L LASG +L Sbjct: 237 PKEAMCVVTEELSRGYIGVGSL-GTRSEIAAELIIGGGTDEQKAHYLPKLASGEILPTAV 295 Query: 123 LTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSA-GKRGISA 181 TEP GSD +SL+TRA GD Y ++G K +IT A ++ + T+P+ G +G+S Sbjct: 296 FTEPNTGSDLASLRTRAVKEGDVYKVSGNKTWITHPVRADLMTLLVRTNPAEPGYKGLSM 355 Query: 182 FIV---------PTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGE-EGEGYK 231 + P + G +E LG +I F+ +VP LG EG+G+K Sbjct: 356 LLAEKPRGTDEDPFPAKGMTGGEIE-VLGYRGMKEFEIGFDGFEVPAGQLLGGVEGQGFK 414 Query: 232 IALANLEGGRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIA 291 + E R+ A+++VG+A+AA E YA ER FGKP+I VA ++ MA +IA Sbjct: 415 QLMNTFEAARIQTAARAVGVAQAAMETGLRYAEERIQFGKPLIAFPRVADKIVMMAVEIA 474 Query: 292 VARQMVHYAAALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIY 351 +ARQ+ ++AA +D G+ +EA M+KL + +A ALQ GG G+ ++ + R+ Sbjct: 475 IARQITYFAARAKDEGRRTDLEAGMSKLLGARVAWAAADNALQIHGGNGFALEYQVSRLL 534 Query: 352 RDVRVCQIYEGTSDIQRMVISRNL 375 D R+ I+EG ++IQ VI+R L Sbjct: 535 CDARILNIFEGAAEIQAQVIARRL 558 Score = 29.6 bits (65), Expect = 2e-04 Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 4/89 (4%) Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIE----HQAVAFRLADMATQIAVARQMVHY 299 + S + RA +A + + S GK E Q LA +AT + R+++HY Sbjct: 21 VRSALPALERALTDATQAVREKVSSGGKLSAELLESEQRAVHGLAWLATYVFGVRELLHY 80 Query: 300 AAALRDSGKPALVEASMAKLFASEMAEKV 328 A L SGK E + ++ A E ++ Sbjct: 81 ADRLGASGKFGEAERLIVQIGAGEYIAQI 109 Lambda K H 0.319 0.134 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: 454 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 564 Length adjustment: 33 Effective length of query: 342 Effective length of database: 531 Effective search space: 181602 Effective search space used: 181602 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: 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