Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 201485 SO2341 alpha keto acid dehydrogenase complex, E2 component (NCBI ptt file)
Query= reanno::Marino:GFF1672 (378 letters) >FitnessBrowser__MR1:201485 Length = 535 Score = 378 bits (971), Expect = e-109 Identities = 209/388 (53%), Positives = 264/388 (68%), Gaps = 11/388 (2%) Query: 1 MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60 MTDKA+V+I A KAG++ KL++++ +AKVHAPL+A P + + A +T Sbjct: 147 MTDKALVQIPAIKAGKIVKLHYRKGQLAKVHAPLYAIEVEGGVIPAVSAHETTNVAVANT 206 Query: 61 ATASPVAAASRQRIPA-------SPAVRRLVREHELNLSDIQGSGKDGRVLKADVLAYIE 113 AT++ A AS + PA SPAVRR+ R +++LS + GSGK GRV K D+ + Sbjct: 207 ATSAACATASVSQEPARQGKALASPAVRRMARALDIDLSRVPGSGKHGRVYKEDISRFQA 266 Query: 114 EGPKQ--AQNQAPADDAQTATTRSARRAPAADQEAR--VEPIRGIKAAMAKSMVKSATTI 169 +G A A Q++ T+SA A VEPIRG+KA MAK MV+S +TI Sbjct: 267 QGSATPVVAPVATASTQQSSVTQSAVPITVASAARADIVEPIRGVKAVMAKLMVESVSTI 326 Query: 170 PHFIYSEDIDVTDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEFPVLNSQLNDDV 229 PHF Y E+ D+TDL+ LRE +K + + +LT+MPFFMKAM+LA+ +FPVLNSQ+N D Sbjct: 327 PHFTYCEEFDLTDLVALRESMKAKYSSDEVKLTMMPFFMKAMSLALTQFPVLNSQVNADC 386 Query: 230 TEIHYLPQCNIGMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAARSGRVSQEDLKG 289 TEI Y + NIGMAVD K GL VPN+K V+ S+L +A E+ RLT AARSGRV+ DLK Sbjct: 387 TEITYKARHNIGMAVDSKVGLLVPNVKDVQDKSILEVAAEITRLTNAARSGRVAPADLKE 446 Query: 290 GTITISNIGALGGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVERAIMTVSWAGDHR 349 GTI+ISNIGALGGT PIIN PEVAIVALG+ Q LPRF+A G+V R IM VSW+GDHR Sbjct: 447 GTISISNIGALGGTVATPIINKPEVAIVALGKLQTLPRFNAKGEVEARQIMQVSWSGDHR 506 Query: 350 IIDGGTIARFCNRWKGYLESPQTMLLHM 377 +IDGGTIARFCN WK YLE PQ MLL M Sbjct: 507 VIDGGTIARFCNLWKQYLEQPQDMLLAM 534 Score = 53.5 bits (127), Expect = 1e-11 Identities = 32/70 (45%), Positives = 46/70 (65%), Gaps = 2/70 (2%) Query: 1 MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60 MTDKA+V+I AP AG VTKLY+ + +AKVHAPL+A + + EEP ++ P+ + Sbjct: 40 MTDKALVQIPAPFAGVVTKLYYAKGDIAKVHAPLYA-VQIEAEEP-SSQVAPQTVEHSAP 97 Query: 61 ATASPVAAAS 70 A+ AA+S Sbjct: 98 NQAAISAASS 107 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: 476 Number of extensions: 20 Number of successful extensions: 4 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: 535 Length adjustment: 33 Effective length of query: 345 Effective length of database: 502 Effective search space: 173190 Effective search space used: 173190 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 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