Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_076582964.1 BB347_RS13025 2-oxo acid dehydrogenase subunit E2
Query= reanno::Marino:GFF1672 (378 letters) >NCBI__GCF_001971705.1:WP_076582964.1 Length = 541 Score = 196 bits (499), Expect = 1e-54 Identities = 118/341 (34%), Positives = 190/341 (55%), Gaps = 14/341 (4%) Query: 46 EEARTKPEPA-AQLSTATASP---VAAASRQRIPASPAVRRLVREHELNLSDIQG-SGKD 100 + A T+ P + +S AT++P + A R++ A+PA RR+ E +N+ + +D Sbjct: 203 DRAGTEATPTTSSVSGATSAPSTDLEDADREQTLAAPATRRIAEEEGVNIDAVPAVEERD 262 Query: 101 GR-VLKADVLAYIEEGPKQAQNQAPADDAQTATTRSARRAPAADQEA-RVEPIRGIKAAM 158 G+ + D + E +Q A ++ + A +D E R EP G++ Sbjct: 263 GQPFVTPDAVREYAEAKRQG---AESEGLEAGGAADATGVDFSDGERERREPFAGVRKRT 319 Query: 159 AKSMVKSATTIPHFIYSEDIDVTDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEF 218 A +MV+S T PH + +++DVT L++ RE LKP A RG RLT MPF +KA+ A++E+ Sbjct: 320 ADAMVESKFTAPHVTHHDEVDVTALVEAREDLKPRAADRGIRLTYMPFIVKAVVAALKEY 379 Query: 219 PVLNSQLNDDVTEIHYLPQCNIGMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAAR 278 P +N+ ++DD EI Y N+G+A AGL VP ++ + LL +A + L + AR Sbjct: 380 PEMNAVIDDDAEEIVYRDYYNVGIATATDAGLLVPVVENADQQGLLALASSMNELVQKAR 439 Query: 279 SGRVSQEDLKGGTITISNIGALGGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVE-- 336 VS +L+G T T++N+G +GG Y PI+N PE I+A+G ++ PR + + E Sbjct: 440 ERTVSPTELQGSTFTVTNVGGIGGEYATPILNYPEAGILAVGEIKRKPRVVTDEEGTETI 499 Query: 337 --RAIMTVSWAGDHRIIDGGTIARFCNRWKGYLESPQTMLL 375 R+++T+S + DHR+IDG A+F N LE+P +LL Sbjct: 500 EPRSVLTLSLSFDHRLIDGAIGAQFMNTVMESLENPHLLLL 540 Score = 57.4 bits (137), Expect = 9e-13 Identities = 56/204 (27%), Positives = 86/204 (42%), Gaps = 36/204 (17%) Query: 2 TDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPL--FAFIPRDREEPE------EARTKPE 53 TDKA+VE+ +P G V++L++ + + V FA D E E A + E Sbjct: 41 TDKALVEVPSPVDGTVSELHYAEGDVIPVGNVFVTFALEGEDAETAEPDSGSASADEETE 100 Query: 54 PAAQLSTA-------TASPVAAAS--------RQRIPASPAVRRLVREHELNLSDIQGSG 98 P +A SP A + + R+ P +RR RE L+LS ++GSG Sbjct: 101 PTTDAESAPTDEESEAGSPGAIGADTEETGTPQDRVFVPPRLRRKAREDGLDLSSVRGSG 160 Query: 99 KDGRVLKADVLAYIEEGPKQAQNQAPADDAQTATTRSARRAPAADQEARVEPIRGIKAAM 158 GR+ AD+ +A + A +T + S+ A D V+ G +A Sbjct: 161 PGGRITAADI---------RAASAADDGGQETPDSGSSDTETAGDSSDTVDDRAGTEATP 211 Query: 159 AKSMVKSATTIPHFIYSEDIDVTD 182 S V AT+ P S D++ D Sbjct: 212 TTSSVSGATSAP----STDLEDAD 231 Lambda K H 0.316 0.131 0.367 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: 452 Number of extensions: 16 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 378 Length of database: 541 Length adjustment: 33 Effective length of query: 345 Effective length of database: 508 Effective search space: 175260 Effective search space used: 175260 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