Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 7024958 Shewana3_2129 dihydrolipoamide acetyltransferase (RefSeq)
Query= reanno::Marino:GFF1672 (378 letters) >FitnessBrowser__ANA3:7024958 Length = 531 Score = 381 bits (978), Expect = e-110 Identities = 214/391 (54%), Positives = 267/391 (68%), Gaps = 23/391 (5%) Query: 1 MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60 MTDKA+V+I A KAG++ KL++++ +AKVHAPLFA E E + P AQ ++ Sbjct: 149 MTDKALVQIPAIKAGKIVKLHYRKGQLAKVHAPLFAI------EVEGGVSAPVSHAQEAS 202 Query: 61 ATA----SPVAAASRQRIPA-------SPAVRRLVREHELNLSDIQGSGKDGRVLKADVL 109 ATA +PVA A+ PA SPAVRR+ R +++LS + GSGK GRV K D+ Sbjct: 203 ATAVNTAAPVACAAVSSEPARQGKALASPAVRRMARALDIDLSRVPGSGKHGRVYKEDIT 262 Query: 110 AYIEEG---PKQAQNQAPADDAQTATTRSARRAPAADQEARVEPIRGIKAAMAKSMVKSA 166 + +G P A A AQ+ + + A D VEPIRG+KA MAK MV+S Sbjct: 263 RFQAQGGAVPAAAPVAAAPTVAQSTVSTAVASAARGDI---VEPIRGVKAVMAKMMVESV 319 Query: 167 TTIPHFIYSEDIDVTDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEFPVLNSQLN 226 +TIPHF Y E+ D+TDL+ LRE +K + + +LT+MPFFMKAM+LA+ +FPVLNSQ+N Sbjct: 320 STIPHFTYCEEFDLTDLVALRESMKAKYSSDEVKLTMMPFFMKAMSLALTQFPVLNSQVN 379 Query: 227 DDVTEIHYLPQCNIGMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAARSGRVSQED 286 D TEI Y + NIGMAVD K GL VPN+K V+ S+L +A E+ RLT AARSGRV+ D Sbjct: 380 ADCTEITYKARHNIGMAVDSKVGLLVPNVKDVQDKSILEVAAEITRLTNAARSGRVAPAD 439 Query: 287 LKGGTITISNIGALGGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVERAIMTVSWAG 346 LK GTI+ISNIGALGGT PIIN PEVAIVALG+ Q LPRF+A G+V R IM VSW+G Sbjct: 440 LKEGTISISNIGALGGTVATPIINKPEVAIVALGKLQTLPRFNAKGEVEARQIMQVSWSG 499 Query: 347 DHRIIDGGTIARFCNRWKGYLESPQTMLLHM 377 DHR+IDGGTIARFCN WK YLE PQ MLL M Sbjct: 500 DHRVIDGGTIARFCNLWKQYLEQPQDMLLAM 530 Score = 56.6 bits (135), Expect = 2e-12 Identities = 33/70 (47%), Positives = 44/70 (62%), Gaps = 4/70 (5%) Query: 1 MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60 MTDKA+V+I AP AG VTKLY+ + +AKVHAPL+A E A ++PE T Sbjct: 40 MTDKALVQIPAPFAGVVTKLYYTKGDIAKVHAPLYAVQIESDEAAPVAASQPE----AHT 95 Query: 61 ATASPVAAAS 70 AT +P + +S Sbjct: 96 ATQTPASQSS 105 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: 503 Number of extensions: 22 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: 531 Length adjustment: 33 Effective length of query: 345 Effective length of database: 498 Effective search space: 171810 Effective search space used: 171810 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