Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_057509244.1 ABB28_RS14005 acyl-CoA dehydrogenase
Query= BRENDA::Q92947 (438 letters) >NCBI__GCF_001431535.1:WP_057509244.1 Length = 387 Score = 367 bits (943), Expect = e-106 Identities = 193/376 (51%), Positives = 254/376 (67%), Gaps = 4/376 (1%) Query: 60 LTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREIISEMGELGVLGPTIK-GYGCAGV 118 L+ +E ++D+ + +R++P I F E++ E+ LG+LG T+ YG G+ Sbjct: 15 LSDEERAVQDSVARFVDQRVLPVIGDCFDQARFPAELVPEIAALGLLGATLPPAYGGGGM 74 Query: 119 SSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQRQKYLPQLAKGELLGCFG 178 +VAYGL+ +ELER DSG RS +SVQSSL MHPI+AYGSE QR ++LP +A+GE +GCFG Sbjct: 75 DAVAYGLICQELERGDSGLRSFVSVQSSLCMHPIFAYGSEAQRLRWLPAMARGERIGCFG 134 Query: 179 LTEPNSGSDPSSMETRAHYNSSNKSYTLNGTKTWITNSPMADLFVVWARCEDGCIRGFLL 238 LTE + GSDPSSM+TRA + L+G+K WITN+P+ADL +VWA+ EDG ++GF+L Sbjct: 135 LTEAHGGSDPSSMKTRAVREGDQ--WRLDGSKMWITNAPIADLAIVWAQTEDG-VQGFIL 191 Query: 239 EKGMRGLSAPRIQGKFSLRASATGMIIMDGVEVPEENVLPGASSLGGPFGCLNNARYGIA 298 E+GM G S I K SLRAS+TG + D V+VPE N L G + GP GCLN AR+GI+ Sbjct: 192 ERGMAGFSVQEIGRKMSLRASSTGALFFDQVQVPEANRLAGVVGMKGPLGCLNQARFGIS 251 Query: 299 WGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKLADMLTEITLGLHACLQLGRLKD 358 WG +GA+ CL YA R FG PLA Q Q KLADM IT LQLGRLK+ Sbjct: 252 WGPIGAAIACLREVLAYAGQRELFGRPLAATQSAQIKLADMARRITGAQLLALQLGRLKE 311 Query: 359 QDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVNTYEGTHD 418 + P+ VSL K NNC A+DIAR+ RD+LG GI+ E+ IRHA+NLE+V TYEGT Sbjct: 312 AGRLQPQQVSLAKWNNCRMAIDIARECRDLLGAAGITTEHAAIRHALNLESVITYEGTET 371 Query: 419 IHALILGRAITGIQAF 434 +H L++GR +TG+ AF Sbjct: 372 VHQLVIGRELTGLTAF 387 Lambda K H 0.319 0.135 0.400 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: 471 Number of extensions: 15 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: 438 Length of database: 387 Length adjustment: 31 Effective length of query: 407 Effective length of database: 356 Effective search space: 144892 Effective search space used: 144892 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