Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_067911252.1 AQZ52_RS12615 pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase
Query= reanno::pseudo6_N2E2:Pf6N2E2_479 (423 letters) >NCBI__GCF_001519075.1:WP_067911252.1 Length = 430 Score = 196 bits (499), Expect = 9e-55 Identities = 141/429 (32%), Positives = 214/429 (49%), Gaps = 19/429 (4%) Query: 6 IKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGRVIALGGEPG 65 IKMP + + E L+ W VKVGD V ++A++ TDKA ++ + G V+A+ G Sbjct: 5 IKMPALSPTMEEGTLAKWLVKVGDKVSSGDIMAEIETDKATMEFEAVDEGTVVAIEVAEG 64 Query: 66 -EVMAVGSELIRIEVEGAGNLKESAQQAPTPTPAAQAPKPAPVATPEPVLEKTAAPRCAP 124 E + VG+ + I E G+ +A P PA AP PAPVA P AAP AP Sbjct: 65 TEGVKVGTVIATIAGEDDGDAAPAAAAVSAPAPAPVAPMPAPVAAPAAA-PVAAAPAPAP 123 Query: 125 QAPVARDPDERPLASPAVRKHALDLGIQLRLVQGSGPAGRVLHEDLE--------AYLAQ 176 APVA D R +ASP ++ A + GI L V GSGP GR++ DL+ A A Sbjct: 124 -APVAAAGD-RIVASPLAKRIASEKGIDLGTVTGSGPHGRIIKADLDVAAPKAAVAAPAA 181 Query: 177 GPS-----VQAKGGSGYAERHDEQQIPVIGMRRKIAQRMQEATQRAAHFSYVEEIDITAL 231 P+ V A + ++ + + + MR+ IA+R+ EA H+ +I + L Sbjct: 182 VPAPVAAPVAAPAAAPFSTDIPHEAVKLSSMRKTIARRLTEAKATVPHYYLTVDISLDKL 241 Query: 232 EELRVHLNEKHGASRGKLTLLPFLVRALVVALRDFPQMNARYDDEAQVIHRSGAVHVGVA 291 +LR LN KL++ L++AL AL P N + + + R + VA Sbjct: 242 LKLRAELNAALAGEGVKLSVNDLLIKALGKALMLAPDANVSFAGDNLI--RYSRADIAVA 299 Query: 292 TQSDVGLMVPVVRHAEARSLWDNAAEISRLATAARTGKASRDELSGSTITLTSLGALGGI 351 GL+ P+V A+ +S+ +++ LA A+ GK + E G T +L++LG G Sbjct: 300 VSIPGGLITPIVTGADVKSISAIQKDMADLAARAKAGKLAPHEYQGGTASLSNLGMFGIK 359 Query: 352 VSTPVLNLPEVAIVGVNKIVERPVVIKGQIVIRKMMNLSSSFDHRVVDGMDAAQFIQALR 411 V+N P+ I+ + +RP VI + I +M+ + SFDHR +DG + AQ +QA + Sbjct: 360 QFVAVINPPQGMIMAIGAGEKRPYVIDDALGIATVMSATGSFDHRAIDGAEGAQLMQAFK 419 Query: 412 GLLEQPATL 420 L+E P L Sbjct: 420 TLVEAPLAL 428 Lambda K H 0.317 0.133 0.375 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: 439 Number of extensions: 32 Number of successful extensions: 7 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: 423 Length of database: 430 Length adjustment: 32 Effective length of query: 391 Effective length of database: 398 Effective search space: 155618 Effective search space used: 155618 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