Align Lipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; EC 2.3.1.168; Branched-chain alpha-keto acid dehydrogenase complex component E2; BCKAD-E2; BCKADE2; Dihydrolipoamide acetyltransferase component of branched-chain alpha-keto acid dehydrogenase complex; Dihydrolipoamide branched chain transacylase; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (uncharacterized)
to candidate N515DRAFT_2777 N515DRAFT_2777 2-oxoglutarate dehydrogenase E2 component
Query= curated2:P37942 (424 letters) >FitnessBrowser__Dyella79:N515DRAFT_2777 Length = 400 Score = 245 bits (625), Expect = 2e-69 Identities = 159/416 (38%), Positives = 233/416 (56%), Gaps = 24/416 (5%) Query: 1 MAIEQMTMPQLGESVTEGTISKWLVAPGDKVNKYDPIAEVMTDKVNAEVPSSFTGTITEL 60 M+IE + +P L ESV++ TI+ W G+ + + + + ++ TDKV EVP+ G I EL Sbjct: 1 MSIE-VKVPVLPESVSDATIATWHKKVGEAIKRDENLVDLETDKVVLEVPAPVDGVIKEL 59 Query: 61 VGEEGQTLQVGEMICKIETEGANPAEQKQEQPAASEAAENPVAKSAGAADQPNKKRYSPA 120 + G T+ ++I IE EGA A PAA+ AA A +A AA SPA Sbjct: 60 KFQSGDTVTSQQVIAVIE-EGAVAAAPA---PAAAPAAAPAPAAAAPAAPAKGTADLSPA 115 Query: 121 VLRLAGEHGIDLDQVTGTGAGGRITRKDIQRLIETGGVQEQNPEELKTAAPAPKSASKPE 180 LR+A E ID +V GTG GR+T++D+ + G AA AP A+KP Sbjct: 116 GLRVATEQNIDPSKVAGTGRDGRVTKEDLVNYGKGGAAAP--------AAAAP--AAKPT 165 Query: 181 PKEETSYPASAAGDKEIPVTGVRKAIASNMKRSKTEIPHAWTMMEVDVTNMVAYRNSIKD 240 P A ++ +P+T +R IA + +SK I + EV++ +V R ++ + Sbjct: 166 P--------GARPEERVPMTRIRARIAERLMQSKNSIAMLTSFNEVNLAEVVKMRKTLGE 217 Query: 241 SFKKTEGFNLTFFAFFVKAVAQALKEFPQMNSMWAGDKIIQKKDINISIAVATEDSLFVP 300 F+K+ G L F +FFVKA A+ALK P +N+ G+ I+ +ISIAV+T+ L P Sbjct: 218 QFEKSNGVKLGFMSFFVKAAAEALKRHPVVNASVDGNDIVYHGYQDISIAVSTDKGLVTP 277 Query: 301 VIKNADEKTIKGIAKDITGLAKKVRDGKLTADDMQGGTFTVNNTGSFGSVQSMGIINYPQ 360 V+++ +K+ I K I AKK RDGKL DD+QGGTFT+ N G+FGS+ S I+N PQ Sbjct: 278 VLRDVQDKSFADIEKGILDYAKKARDGKLGLDDLQGGTFTITNGGTFGSLLSTPIVNPPQ 337 Query: 361 AAILQVESIVKRPVVMDNGMIAVRDMVNLCLSLDHRVLDGLVCGRFLGRVKQILES 416 +AIL + +I R +V +NG + M+ L LS DHR++DG FL +K LE+ Sbjct: 338 SAILGMHTIKDRAIV-ENGQVIAAPMMYLALSYDHRIIDGKDAVLFLVDIKNQLEN 392 Lambda K H 0.312 0.129 0.359 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: 408 Number of extensions: 21 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: 424 Length of database: 400 Length adjustment: 31 Effective length of query: 393 Effective length of database: 369 Effective search space: 145017 Effective search space used: 145017 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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