Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_085219205.1 B9N75_RS13160 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >NCBI__GCF_900177405.1:WP_085219205.1 Length = 383 Score = 186 bits (471), Expect = 1e-51 Identities = 121/382 (31%), Positives = 195/382 (51%), Gaps = 10/382 (2%) Query: 14 LDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYG 73 LD L + +RD +A+ ++AP + + ++ EMG +GL G T+ E+ G Sbjct: 6 LDFALGEMADTIRDTTRRFAEDRIAPLAAKIDAEDWFPTELWPEMGALGLHGITVAEEDG 65 Query: 74 GPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWI 133 G GL Y+ + + EV R + S+L + I + + QK +YLPKL +GE + Sbjct: 66 GLGLGYLEHVVAQEEVARASASIGLSYGAHSNLCVNQIRRWANAEQKARYLPKLISGEHV 125 Query: 134 GCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDEI 193 G ++E GSD SM +A K Y L+G+K WITN+ AD VV+AK E R I Sbjct: 126 GSLAMSEAGAGSDVVSMKLKAEKKGDRYVLNGTKFWITNAAYADTLVVYAKTGEGSRG-I 184 Query: 194 RGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCLNS 252 F++EK KG + K+G+R S T E++ D+ VPEEN++ P G+ + L+ Sbjct: 185 TTFLIEKDMKGFAIGQKLDKMGMRGSPTAELLFDDCEVPEENVMGPENGGVGVLMSGLDY 244 Query: 253 ARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLR 312 R +A LG ++C + +V +RKQFG+ + + QLIQ K+ADM + V Sbjct: 245 ERTVLAGIQLGIMQACLDVVIPFVRERKQFGKAIGSFQLIQAKVADMYVALNSARAYVYA 304 Query: 313 LGRMKDEGTA----AVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLE 368 + R D G A + N+ +L+ A LGG G + ++ V R+ + + Sbjct: 305 VARACDAGKTTRFDAAGAILLASENAVKSSLE----AIQALGGAGYTKDWPVERYARDAK 360 Query: 369 VVNTYEGTHDIHALILGRAQTG 390 +++ GT++I +++GR G Sbjct: 361 LLDIGAGTNEIRRMLIGRELIG 382 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: 333 Number of extensions: 13 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: 383 Length adjustment: 30 Effective length of query: 365 Effective length of database: 353 Effective search space: 128845 Effective search space used: 128845 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 24 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