Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate 5209456 Shew_1927 dihydrolipoamide acetyltransferase (RefSeq)
Query= reanno::Marino:GFF1672 (378 letters) >FitnessBrowser__PV4:5209456 Length = 520 Score = 367 bits (942), Expect = e-106 Identities = 198/377 (52%), Positives = 255/377 (67%), Gaps = 5/377 (1%) Query: 1 MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60 MTDKA+V+I A K+G+V KL++++ +A+VH PLF+ E A A + Sbjct: 148 MTDKALVQIPAIKSGKVVKLHYRKGQLAQVHTPLFSIEVESEEGIVAAPVADTAPAAVDH 207 Query: 61 ATASPVAAASRQRIPASPAVRRLVREHELNLSDIQGSGKDGRVLKADVLAYIEEGPKQAQ 120 A A + ASPAVRRL R ++++LS + GSGK GRV K DV + + + Sbjct: 208 EEVELHAPAGNGKALASPAVRRLARSYDIDLSLVPGSGKHGRVYKEDVERF--RSGEAVK 265 Query: 121 NQAPADDAQTATTRSARRAPAADQEARVEPIRGIKAAMAKSMVKSATTIPHFIYSEDIDV 180 +A AQ+ T + A D RVEPIRG+KA MAK M +S +TIPHF Y E++D+ Sbjct: 266 AKAAKAQAQSEPTAAPIAVSAGD---RVEPIRGVKAVMAKMMTESVSTIPHFTYCEELDL 322 Query: 181 TDLLKLREQLKPEAEARGSRLTLMPFFMKAMALAVQEFPVLNSQLNDDVTEIHYLPQCNI 240 T+L+ LRE +K + +LT+MPFFMKAM+LA+ +FP +NS++NDD TE +L NI Sbjct: 323 TELVALRESMKARYSSDDLKLTMMPFFMKAMSLALTQFPGINSRVNDDCTEQTFLASHNI 382 Query: 241 GMAVDGKAGLTVPNIKGVESLSLLGIADEVARLTEAARSGRVSQEDLKGGTITISNIGAL 300 GMAVD K GL VPN+K V+ S+L +A E+ RLT+ ARSGRVS DLKGG+I+ISNIGAL Sbjct: 383 GMAVDSKVGLLVPNVKDVQQKSILEVAAEITRLTKDARSGRVSPADLKGGSISISNIGAL 442 Query: 301 GGTYTAPIINAPEVAIVALGRTQKLPRFDANGQVVERAIMTVSWAGDHRIIDGGTIARFC 360 GGT PIIN PEVAIVALG+ Q LPRF+ G+V R IM +SW+GDHR+IDGGTIARFC Sbjct: 443 GGTVATPIINKPEVAIVALGKLQTLPRFNDKGEVEARKIMQISWSGDHRVIDGGTIARFC 502 Query: 361 NRWKGYLESPQTMLLHM 377 N WK YLESPQ MLL M Sbjct: 503 NLWKQYLESPQEMLLAM 519 Score = 40.0 bits (92), Expect = 1e-07 Identities = 27/89 (30%), Positives = 45/89 (50%), Gaps = 1/89 (1%) Query: 1 MTDKAMVEITAPKAGRVTKLYHQQQAMAKVHAPLFAFIPRDREEPEEARTKPEPAAQLST 60 MTDKA+V+I A G + KL++++ +A VH PL++ + D E +A T+ + Sbjct: 40 MTDKALVQIPAVHGGVIKKLHYKKGDIAIVHEPLYS-VEIDGELDGDATTESAAEEAVVQ 98 Query: 61 ATASPVAAASRQRIPASPAVRRLVREHEL 89 + + PV R P + + E EL Sbjct: 99 SDSQPVVGGKRVEEFLLPDIGEGIVECEL 127 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: 505 Number of extensions: 21 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: 520 Length adjustment: 32 Effective length of query: 346 Effective length of database: 488 Effective search space: 168848 Effective search space used: 168848 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