Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_111393848.1 CLV31_RS15640 acyl-CoA dehydrogenase
Query= BRENDA::Q92947 (438 letters) >NCBI__GCF_003253485.1:WP_111393848.1 Length = 401 Score = 399 bits (1026), Expect = e-116 Identities = 204/398 (51%), Positives = 278/398 (69%), Gaps = 4/398 (1%) Query: 39 QLAKSSRPE-FDWQDPLVLEEQLTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREII 97 ++ KS + + F+ D L L++ LT ++ LIR + R + ++ + P I + F EI+ Sbjct: 5 EIQKSLKQDLFEGVDFLDLDDLLTEEQKLIRSSIRDFVKKEISPYIEDWAQKAHFPYEIV 64 Query: 98 SEMGELGVLGPTIK-GYGCAGVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYG 156 + GE+G GP + YGC G+ ++YGL+ +E+ER DSG RS SVQ SLVM+PIY +G Sbjct: 65 KKFGEVGAFGPQLPVEYGCGGLDYISYGLIMQEIERGDSGMRSTASVQGSLVMYPIYKFG 124 Query: 157 SEEQRQKYLPQLAKGELLGCFGLTEPNSGSDPSSMETRAHYNSSNKSYTLNGTKTWITNS 216 +EEQR KYLP+LA GELLGCFGLTEP+ GS+PS M T ++ Y LNG K WI+NS Sbjct: 125 TEEQRLKYLPRLASGELLGCFGLTEPDHGSNPSGMVT--NFKDMGDHYLLNGAKMWISNS 182 Query: 217 PMADLFVVWARCEDGCIRGFLLEKGMRGLSAPRIQGKFSLRASATGMIIMDGVEVPEENV 276 P AD+ VVWA+ E+G I+G ++E+GM G S P K+SLRAS TG ++ D V+VP+EN+ Sbjct: 183 PKADIAVVWAKNEEGRIQGLIVERGMEGFSTPETHNKWSLRASCTGELVFDNVKVPKENL 242 Query: 277 LPGASSLGGPFGCLNNARYGIAWGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKL 336 LPG + LG P CL++AR+GIAWG +GA+ C +AR+YA +R+QFG P+ QL QKKL Sbjct: 243 LPGKTGLGAPMMCLDSARFGIAWGAIGAAMDCYESARRYAAERIQFGKPIGGFQLTQKKL 302 Query: 337 ADMLTEITLGLHACLQLGRLKDQDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISD 396 A+MLTEIT ++G++ ++ KA +S+ KRNN AL+IAR+AR + GG GI+ Sbjct: 303 AEMLTEITKAQLLAWKVGKMMNEGKAKTVHISMAKRNNVEMALNIAREARQIHGGMGITG 362 Query: 397 EYHVIRHAMNLEAVNTYEGTHDIHALILGRAITGIQAF 434 EY ++RH MNLE+V TYEGTHDIH LILG ITGIQAF Sbjct: 363 EYPIMRHMMNLESVITYEGTHDIHLLILGNEITGIQAF 400 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: 468 Number of extensions: 18 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: 401 Length adjustment: 32 Effective length of query: 406 Effective length of database: 369 Effective search space: 149814 Effective search space used: 149814 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