Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate PfGW456L13_2983 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= BRENDA::Q3JP94 (395 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2983 Length = 375 Score = 206 bits (525), Expect = 7e-58 Identities = 126/369 (34%), Positives = 189/369 (51%), Gaps = 2/369 (0%) Query: 20 DDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGLDY 79 DD++ +RD A +AQ +L P E R EM +G G +PEQ+GG Y Sbjct: 5 DDQQQIRDMARDFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64 Query: 80 VSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFGLT 139 ++Y + E+ D ++MSV +S+ VPI +G+D QKE++L LA+G +G F LT Sbjct: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILNYGTDEQKERFLKPLASGAMLGAFALT 124 Query: 140 EPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDED-GRDEIRGFIL 198 EP GSD + TRAR Y L+G K +IT+ A V +V+A D G+ I FI+ Sbjct: 125 EPQAGSDASGLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIV 184 Query: 199 EKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCLNSARYGI 257 G + K+G AS T +I+ ++ VP N L +G R L R GI Sbjct: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPLANRLGEEGEGYRIALANLEGGRVGI 244 Query: 258 AWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMK 317 A ++G A + + AR Y +R+ FG+P+ +Q + +LADM T+I + Q V ++ Sbjct: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 Query: 318 DEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEGTH 377 D G A+ S+ K + A + A LGG G ++F V R ++ V YEGT Sbjct: 305 DSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPVERIYRDVRVCQIYEGTS 364 Query: 378 DIHALILGR 386 DI +++ R Sbjct: 365 DIQRMVISR 373 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: 337 Number of extensions: 13 Number of successful extensions: 3 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: 375 Length adjustment: 30 Effective length of query: 365 Effective length of database: 345 Effective search space: 125925 Effective search space used: 125925 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