Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_051305500.1 G494_RS0107600 2-oxo acid dehydrogenase subunit E2
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3542 (425 letters) >NCBI__GCF_000429965.1:WP_051305500.1 Length = 444 Score = 213 bits (541), Expect = 1e-59 Identities = 152/464 (32%), Positives = 228/464 (49%), Gaps = 63/464 (13%) Query: 1 MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIAL 60 M T MPD+GEGI E E+ V++G V E Q + ++ TDKA V+IPSPV G V + Sbjct: 1 MSTTSFFMPDLGEGIHEAEVLSILVELGQEVKEGQTILEMETDKAAVEIPSPVTGVVTEI 60 Query: 61 GGQPGEVMAVGSVLISIEVEGAGNV----KESAQPAPVVKEAPVAATKVETVVESKPVAA 116 Q G ++AVG VL+ + V S P P + A A + Sbjct: 61 AVQAGAMVAVGQVLLVFTTDDRAGVPAEQNRSTAPGPEPEPAGEGAG-----------SK 109 Query: 117 PAPKAAVCQGPMVAREADERPLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDAYLA 176 P+P +G +V ASPA R+ A +LGI+L+LV +G AG V +D+ A+ A Sbjct: 110 PSPG----RGKIVP--------ASPASRRLARELGIELQLVPPSGAAGLVTADDIRAFAA 157 Query: 177 QGQSN-----------------------ASAPVAAAYAQRT--------DEQQIPVIGMR 205 Q + A+APV + A +++P +R Sbjct: 158 QEAARTVPPSSGEQASGETAPPGGMVPEAAAPVPSTSAGEPLRECFPEGQVERLPFRSIR 217 Query: 206 RKIAQRMQDATQRAAHFSYVEEIDVTAVEELRAHLNEKHGATRGKLTLLPFLVRALVVAL 265 R A RM + H + + +D++A+E R E+ GKLT+ F ++A+ AL Sbjct: 218 RATAARMTRSWTEIPHVTCQDSVDISALEAFRQRHREEIAQAGGKLTMTVFALKAVATAL 277 Query: 266 RDFPQINARYDDEAQVITRLGAVHVGIATQADIGLMVPVVRHAEARSLWDSAAEISRLAT 325 +++P NA D +A I H+G+AT + GLMVPV+R + +S+ + A E+ L Sbjct: 278 KNYPHFNASLDLDAGEIIVKHYFHLGVATDTEHGLMVPVIRDVDRKSIRELAIELHELLA 337 Query: 326 AARNGKASRDELSGSTITLTSLGALGGIVSTPVLNLPEVAIVGVNKIVERPMVIKGQ--- 382 AR K +R+EL G T T+T+ GA+GG +P++N PE AI+G+ + +P V+ Sbjct: 338 RARLRKVAREELQGGTFTITNAGAMGGGFFSPIINYPETAILGLGQARLQPAVVTDDQGE 397 Query: 383 --IVIRKMMNLSSSFDHRVVDGMDAALFIQAIRGLLEQPATLFV 424 I R +M + FDHRVVDG DA F+Q + L P L + Sbjct: 398 QGIEPRLIMPIMLCFDHRVVDGADAIRFLQVVIDGLNDPDKLLM 441 Lambda K H 0.318 0.133 0.368 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: 395 Number of extensions: 20 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: 425 Length of database: 444 Length adjustment: 32 Effective length of query: 393 Effective length of database: 412 Effective search space: 161916 Effective search space used: 161916 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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