Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_011385957.1 AMB_RS18215 acyl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >NCBI__GCF_000009985.1:WP_011385957.1 Length = 378 Score = 205 bits (522), Expect = 2e-57 Identities = 124/370 (33%), Positives = 195/370 (52%), Gaps = 2/370 (0%) Query: 20 DDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDY 79 ++++++RD A ++A+ KLAP R EMGE+G LG +P ++ G G DY Sbjct: 5 EEQQLIRDMARSFAREKLAPNAARWDREHLFPTDAIAEMGELGFLGMVVPSEWDGAGTDY 64 Query: 80 VSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLT 139 VSY + E+ ++MSV +S+ +PI +G++AQK+++L +A GE +GCF LT Sbjct: 65 VSYAMAVMEIAAGCGPLSTIMSVHNSVGCMPILTYGTEAQKDEFLRPMARGEKLGCFCLT 124 Query: 140 EPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDEIRGFIL 198 EP GSD S+ TRAR+ Y LSG+K +I+ + V +V+A D + G+ I F++ Sbjct: 125 EPEAGSDAASIRTRARRDGDHYVLSGAKQFISTAKNGQVAIVFAVTDPQAGKRGISAFVV 184 Query: 199 EKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCLNSARYGI 257 G + + K+G S T ++ ++ VP L GL+ L R GI Sbjct: 185 PTDTPGFTVVRVEDKLGQHLSDTCQLAFEDMRVPASRRLGEEGDGLKIALANLEGGRLGI 244 Query: 258 AWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMK 317 A ++G A S A Y +RKQFG+P+ +Q + +LADM T + + Q VL ++ Sbjct: 245 AAQSVGMARSALDHALAYAKERKQFGKPIFEHQAVAFRLADMATRVEVAEQMVLHAASLR 304 Query: 318 DEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTH 377 D G ++ S+ K + A + A + GG G +F V R ++ V YEGT Sbjct: 305 DAGLPCLKEASMAKLFASEMAERVCSDAIQIHGGYGYLADFPVERIYRDVRVCQIYEGTS 364 Query: 378 DIHALILGRA 387 DI L++ RA Sbjct: 365 DIQRLVISRA 374 Lambda K H 0.320 0.138 0.414 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: 322 Number of extensions: 15 Number of successful extensions: 2 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: 395 Length of database: 378 Length adjustment: 30 Effective length of query: 365 Effective length of database: 348 Effective search space: 127020 Effective search space used: 127020 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: 50 (23.9 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