Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate GFF2286 PGA1_c23180 dihydrolipoyllysine-residue acetyltransferase-like protein
Query= reanno::Smeli:SMc03203 (426 letters) >FitnessBrowser__Phaeo:GFF2286 Length = 292 Score = 166 bits (420), Expect = 9e-46 Identities = 104/303 (34%), Positives = 155/303 (51%), Gaps = 33/303 (10%) Query: 140 LASPAVRLRARESGIDLRQVAG------------------TGPAGRITHEDLDLFISRGA 181 +A P+VR AR+ GIDL ++A +GPAG ++ D+D Sbjct: 5 IAPPSVRALARQKGIDLEKLAKELGRTSIVREDLESGKTTSGPAGDTSYWDVD------- 57 Query: 182 EPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVEEVDMTALEDLRATMN 241 +Q G V + + + A +S + + IP +T+ + D+TA+E LR + Sbjct: 58 ---HSQFGSVGEELMSRFAQVA-----AANLSAANALIPQVTHHDRADVTAIEALRKELK 109 Query: 242 RDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHAAVHIGIATQTPAGLT 301 + + KLT L F +AL + + E P NA+ + VHIGIA T GL Sbjct: 110 PEAQARGVKLTALAFQAKALARALREFPRFNASLSPDGKTLTLKGYVHIGIAVDTAHGLM 169 Query: 302 VPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISSLGAIGGIASTPVINH 361 VPVV + +G+W AAE++ LA A+ DE+ G+++TI++LG IGGI TP++N Sbjct: 170 VPVVHDVDRKGLWQIAAEISDLASRAQNRKVGPDEMGGASMTITNLGGIGGIGFTPIVNP 229 Query: 362 PEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAAVFVQRLKTLLETPAL 421 PEVAI+G+ + VWD P ++ L S+DHRVI+G DAA FV L+ P Sbjct: 230 PEVAILGITRTETVTVWDDDTPRPVTMVPLDLSYDHRVINGADAARFVSYFAGLIADPRR 289 Query: 422 IFV 424 I V Sbjct: 290 IMV 292 Lambda K H 0.317 0.133 0.384 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: 290 Number of extensions: 11 Number of successful extensions: 2 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: 426 Length of database: 292 Length adjustment: 29 Effective length of query: 397 Effective length of database: 263 Effective search space: 104411 Effective search space used: 104411 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: 49 (23.5 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