Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_011654334.1 RL_RS28925 2-oxo acid dehydrogenase subunit E2
Query= reanno::Smeli:SMc03203 (426 letters) >NCBI__GCF_000009265.1:WP_011654334.1 Length = 409 Score = 618 bits (1593), Expect = 0.0 Identities = 313/426 (73%), Positives = 353/426 (82%), Gaps = 17/426 (3%) Query: 1 MGEFIIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWL 60 MGEFIIKMPDVGEGVAEAE+VEWHVK GDPVREDMV+AAVMTDKATVEIPSPV G V WL Sbjct: 1 MGEFIIKMPDVGEGVAEAEIVEWHVKTGDPVREDMVIAAVMTDKATVEIPSPVNGTVTWL 60 Query: 61 GAEVGDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEK 120 EVGD +AVKAPLVRIETAG+ E P I + P+A + + E A P P Sbjct: 61 AGEVGDRIAVKAPLVRIETAGDVDEVQPVGISQT--------PIAETPKAEI-AKPAPAA 111 Query: 121 PAPKPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISRG 180 P P PAPA KPLA+P+VRL ARESG+DLRQV TGPAGRI ED++ F+ G Sbjct: 112 PTPAPAPAE--------KPLAAPSVRLFARESGVDLRQVQATGPAGRILREDIEQFLGHG 163 Query: 181 AEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVEEVDMTALEDLRATM 240 P A+ G RKTA EE+++ GLRRRIAEKM LSTSRIPHITYVEEVDMTALE+LRATM Sbjct: 164 TAPATAKNGFARKTATEEIKLTGLRRRIAEKMVLSTSRIPHITYVEEVDMTALEELRATM 223 Query: 241 NRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHAAVHIGIATQTPAGL 300 N DR+ + KLT+LPFLMRALVK ++EQP VNATFDD AG+I R++AVHIGIATQTPAGL Sbjct: 224 NGDRRADHPKLTVLPFLMRALVKAISEQPDVNATFDDDAGIITRYSAVHIGIATQTPAGL 283 Query: 301 TVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISSLGAIGGIASTPVIN 360 TVPVVRHAEARGIWDCAAE+NRLA+AAR+GTATRDEL+GSTITISSLGA+GGI STP+IN Sbjct: 284 TVPVVRHAEARGIWDCAAEMNRLAEAARSGTATRDELSGSTITISSLGALGGIVSTPIIN 343 Query: 361 HPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAAVFVQRLKTLLETPA 420 PEVAI+GVNKIA RPVWDGAQFVPRK+MNLSSSFDHR+IDGWDAA FVQR++TL+ETPA Sbjct: 344 RPEVAIIGVNKIATRPVWDGAQFVPRKMMNLSSSFDHRIIDGWDAANFVQRIRTLIETPA 403 Query: 421 LIFVEG 426 LIF+EG Sbjct: 404 LIFIEG 409 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: 617 Number of extensions: 16 Number of successful extensions: 2 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: 409 Length adjustment: 32 Effective length of query: 394 Effective length of database: 377 Effective search space: 148538 Effective search space used: 148538 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: 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