Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_013074378.1 BTUS_RS01575 2-oxo acid dehydrogenase subunit E2
Query= reanno::Smeli:SMc03203 (426 letters) >NCBI__GCF_000092905.1:WP_013074378.1 Length = 454 Score = 287 bits (735), Expect = 4e-82 Identities = 179/457 (39%), Positives = 245/457 (53%), Gaps = 36/457 (7%) Query: 1 MGEFIIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWL 60 M +F+ ++PD+GEG+ E E+V W V PGD V ED L V DKA VEIPSPV GKV + Sbjct: 1 MADFVFRLPDIGEGIHEGEIVRWLVNPGDEVDEDQPLCEVQNDKAVVEIPSPVKGKVKEV 60 Query: 61 GAEVGDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKA------ 114 + G T V PLV +ET G A P+ +A Q D P A R + +A Sbjct: 61 KVQAGTTAVVGDPLVVLETEG----ALPEGATKAAGAQQTDGPSAAGGRADGQALSGTGQ 116 Query: 115 -------------PPQPEKPAPKPAPAPREA--PDLSAKPLASPAVRLRARESGIDLRQV 159 + E +PA A + P +A LA+PAVR ARE G+DL +V Sbjct: 117 VQAAVAPTSGKGSDGRGEDWTAEPAGATPDGAEPSGAAMILATPAVRKFAREKGVDLARV 176 Query: 160 AGTGPAGRITHEDLDLFIS--------RGAEPLPAQTGLVRKTAV---EEVRMIGLRRRI 208 GTG GRIT ED+ + R EP + + A E V + G+R+ I Sbjct: 177 RGTGKNGRITREDVLRAAAGPEAEKAERMDEPTAQERAIPMSEAAGLEERVPLAGIRKVI 236 Query: 209 AEKMSLSTSRIPHITYVEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQ 268 A+ M S PH+T ++EVD+T L LR KLT LPF+++A + + Sbjct: 237 AQAMVKSAYTAPHVTVMDEVDVTRLVALRDKAKPLAAERGVKLTYLPFIVKAAIAGLRLH 296 Query: 269 PGVNATFDDHAGVIHRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAAR 328 P +NA+ D+ G I +IGIAT T GL VPVV+ A+ + +W AAE+ LA+ AR Sbjct: 297 PTLNASIDEEKGEIVYKKYYNIGIATDTERGLLVPVVKEADRKNVWMLAAEIRELAEKAR 356 Query: 329 TGTATRDELTGSTITISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKI 388 TG T E+ G T +I+++G GG+ TP+IN+PEVAI+GV +I RPV + Sbjct: 357 TGKLTSPEMKGGTFSITNIGVEGGLFFTPIINYPEVAILGVGRITDRPVVRNGHVAVAPV 416 Query: 389 MNLSSSFDHRVIDGWDAAVFVQRLKTLLETPALIFVE 425 M LS SFDHR++DG +A +V +K LLE P L+ +E Sbjct: 417 MALSLSFDHRLVDGAEAQRYVNDVKRLLEDPDLLTLE 453 Lambda K H 0.317 0.133 0.384 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: 426 Length of database: 454 Length adjustment: 32 Effective length of query: 394 Effective length of database: 422 Effective search space: 166268 Effective search space used: 166268 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 (21.6 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