Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_110205694.1 DNK54_RS04545 AMP-binding protein
Query= metacyc::MONOMER-20125 (556 letters) >NCBI__GCF_003194585.1:WP_110205694.1 Length = 539 Score = 194 bits (492), Expect = 1e-53 Identities = 169/546 (30%), Positives = 250/546 (45%), Gaps = 46/546 (8%) Query: 20 LERAATVYGDCTSVVYDAVS--YTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQM 77 LER + D ++V A +TW + R LA + G+ G + + APN Sbjct: 22 LERTVAAHADREALVEVASGRRWTWREFDRDVNALARGLIGAGVAVGDRIGIWAPNCAAW 81 Query: 78 YELHFAVPMAGAILNAVNLRLDARTISILLHHSE-SKLIFVDHLSRDLILEAIALFPKQA 136 +A GAIL VN + + S S ++ IA ++ Sbjct: 82 TLTQYAAAKVGAILVNVNPAYRTHEFAYAANQSGLSMVVAATRFKESDYAGMIAATAQEC 141 Query: 137 P-VPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPK-----SEWDPMILN 190 P + R+V++ DE+ S++ L+D G+ + + + DP+ + Sbjct: 142 PTIERVVYLDDEA--------------SWQGLLDDGEGVTEDQLRARMDGLAPGDPINIQ 187 Query: 191 YTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYP-WGMAAV 249 YTSGTT PKG HR I + G + +P +H G G + Sbjct: 188 YTSGTTGYPKGATLSHRNILNNGYFTTELIGFTEADRLCIPVPFYHCFGMVMANLGCTSH 247 Query: 250 GGTNICLRK-FDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP--GSEPLKTTVQIMTAGA 306 G T + FD E+ I + + G P + + N P L T + AG+ Sbjct: 248 GATMVIPAPGFDPELTLRAIADERCSAVYGVPTMFIAMQNHPTFADHDLSTLRTGIMAGS 307 Query: 307 PPPSAVLFRT-ESLGFA-VSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGT 364 P V+ R + A V YG+TET+ VSC +++ + T +G Sbjct: 308 ICPVEVMKRCINDMHMAEVGIAYGMTETSP--VSCQTRRDDDLERRTA--------SIGR 357 Query: 365 VM-QTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGD 423 V +I VVDPVTG V R G T GE RG SVMLGY +D E TA+++ ADGW +TGD Sbjct: 358 VHPHVEIKVVDPVTGETVPR-GET-GEFCTRGYSVMLGYWEDSEKTAEAIDADGWMHTGD 415 Query: 424 VGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPC 483 + VM DGY I R KD++I GGEN+ E+E LY+HPDI + V+ PDE +GE C Sbjct: 416 LAVMREDGYANIVGRIKDMVIRGGENIYPREIEEFLYTHPDIEDVQVIGVPDEKYGEELC 475 Query: 484 AFVSLKKGLTKKPTEKEIVE-YCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILR-DMA 541 A+V L+ G P + V + KL + +P+ V+ EE P T TGK++K +R + A Sbjct: 476 AWVKLRAG--ADPLDAAAVRAFATGKLAHFKIPRYVMVVEEFPMTVTGKIRKVQMREESA 533 Query: 542 RGMGSA 547 + +G A Sbjct: 534 QALGLA 539 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: 717 Number of extensions: 47 Number of successful extensions: 5 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: 539 Length adjustment: 36 Effective length of query: 520 Effective length of database: 503 Effective search space: 261560 Effective search space used: 261560 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 24 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