Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate RR42_RS26910 RR42_RS26910 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >FitnessBrowser__Cup4G11:RR42_RS26910 Length = 393 Score = 217 bits (552), Expect = 5e-61 Identities = 133/380 (35%), Positives = 206/380 (54%), Gaps = 7/380 (1%) Query: 14 LDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYG 73 L+ L +D M+R+ +AQ +LAPR E R + +++MG++G+LG T+ E+YG Sbjct: 7 LNFHLGEDIDMLRETVRNWAQAELAPRAAEIDRTDQFPMDAWKKMGDLGVLGITVAEEYG 66 Query: 74 GPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWI 133 G + Y+++ + E+ R + S+L + I G+ AQK +YLPKL +G+WI Sbjct: 67 GANMGYLAHMIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTAAQKARYLPKLVSGDWI 126 Query: 134 GCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDED-GRDE 192 G ++EPN GSD SM RA Y L+G+KMWITN P DV VV+AK + D G Sbjct: 127 GALAMSEPNAGSDVVSMKLRADFKGDHYVLNGTKMWITNGPDCDVLVVYAKTEPDLGARG 186 Query: 193 IRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVK-GLRGPFTCLN 251 + FI+EKG KG S K+G+R S TGE+V + VP ENIL G + + L+ Sbjct: 187 MTAFIVEKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPVENILGGENLGAKVLMSGLD 246 Query: 252 SARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVL 311 R ++ G +G ++C + Y+ DRKQFG+ + QLIQ K+ADM T + + Sbjct: 247 YERAVLSGGPVGIMQACMDVITPYIHDRKQFGQSIGEFQLIQGKVADMYTTLQAARSYLY 306 Query: 312 RLGRM-----KDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVN 366 +G+ KD + + + + KA +A + +LGGNG +E+ V R + Sbjct: 307 TVGKNLDSLGKDHVRQVRKDCAAVILYTAEKATWMAGESVQILGGNGYINEYPVGRLWRD 366 Query: 367 LEVVNTYEGTHDIHALILGR 386 ++ GT +I +++GR Sbjct: 367 AKLYEIGAGTSEIRRMLIGR 386 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: 342 Number of extensions: 12 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: 395 Length of database: 393 Length adjustment: 31 Effective length of query: 364 Effective length of database: 362 Effective search space: 131768 Effective search space used: 131768 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