Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate GFF3780 PGA1_262p01840 ATP-dependent AMP binding enzyme
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__Phaeo:GFF3780 Length = 543 Score = 468 bits (1205), Expect = e-136 Identities = 237/542 (43%), Positives = 342/542 (63%), Gaps = 15/542 (2%) Query: 9 ASSSPLTPLGFLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVS 68 A+ PL+P+ FL RA T++ D +V+Y + TW + R +A+ + SLGI G VS Sbjct: 13 ANYVPLSPVSFLNRAETLHSDRPAVIYGDLRRTWGEVATRIRGVAAGLVSLGIGRGDTVS 72 Query: 69 VLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEA 128 VL PN+P+++EL FA+P+ GA++N +N RL+ TI+ +L H+++K + VD L+ A Sbjct: 73 VLCPNIPELFELQFALPLTGAVINTLNTRLEPETIAYILDHADTKAVIVDRELIPLLSMA 132 Query: 129 IALFPKQAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMI 188 A + V + + D + + + +GK Y++L+ G +P+ EWD + Sbjct: 133 FAAMGRSVSV---IEIDDRNVAAPHTLVGKP----YEELLTDGAGGAPLDLPQDEWDAIA 185 Query: 189 LNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYPWGMAA 248 LNYTSGT+ PKGVV+ HRG ++M + + W P P+YL +PMFH NGW + W MA Sbjct: 186 LNYTSGTSGRPKGVVYHHRGAYLMALGTAAAWQTPHYPIYLSVVPMFHCNGWGHSWVMAM 245 Query: 249 VGGTNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP----GSEPLKTTVQIMTA 304 +GGT + R ++I D I+ HGVTH AP+VL ML+ A + P ++++TA Sbjct: 246 LGGTMVFTRTPSPDLILDAIRSHGVTHFGAAPIVLQMLAEAEAETGSTTPFDPAIKVLTA 305 Query: 305 GAPPPSAVLFRTESLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGT 364 GAPPP +VL +T+++G V YGLTET G + C W+ W E+A+L+++QG+ Sbjct: 306 GAPPPPSVLQKTKAMGLDVMQVYGLTETYGHISKCLWQDSWADKIEAEQAQLQAQQGIAM 365 Query: 365 VMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDV 424 M + V+D TG V RDG T GE+ +RG +VM GY KD + T K+ +GWF++GD Sbjct: 366 PMVEAVSVIDTDTGIPVARDGQTQGEIAVRGNTVMKGYYKDADATDKAF-ENGWFWSGDG 424 Query: 425 GVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPCA 484 V+H DGY++I+DR KDVIISGGEN+SSVEVE++LY HP + AAVVA+PD WGE PCA Sbjct: 425 AVVHADGYMQIRDRLKDVIISGGENISSVEVEAVLYRHPAVQAAAVVAKPDPKWGEVPCA 484 Query: 485 FVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILRDMARGM 544 F+ L+ G T +EI+ +CR+ L + PKTVVF LPKTSTGK+QKF LRD A+ M Sbjct: 485 FIELRTG--SDLTSEEIIAFCRTHLAGFKAPKTVVF-TSLPKTSTGKIQKFQLRDAAKTM 541 Query: 545 GS 546 + Sbjct: 542 ST 543 Lambda K H 0.319 0.135 0.412 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: 837 Number of extensions: 39 Number of successful extensions: 6 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: 556 Length of database: 543 Length adjustment: 36 Effective length of query: 520 Effective length of database: 507 Effective search space: 263640 Effective search space used: 263640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 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