Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 8501639 DvMF_2357 AMP-binding domain protein (RefSeq)
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__Miya:8501639 Length = 550 Score = 175 bits (443), Expect = 5e-48 Identities = 166/565 (29%), Positives = 252/565 (44%), Gaps = 81/565 (14%) Query: 20 LERAATVYGDCTSVVYDAVSYTWSQTHRRCLC----LASSIASLGIENGHVVSVLAPNVP 75 L+ Y D +V+Y V + QT+R+ LA + +LG+ +G V+V A NVP Sbjct: 15 LDETVAKYPDNDAVIY--VDRDYRQTYRQFSQVVDDLAKGLMALGVRHGEKVAVWATNVP 72 Query: 76 QMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFV-----DHLSRDLILEAIA 130 L FA GAIL VN I LL SE + +F+ DH D + Sbjct: 73 YWVALQFATAKMGAILLTVNTNYREHEIRYLLTQSECENLFIIDGFRDH---DYVQTIYN 129 Query: 131 LFPKQAPVPR-------------LVFMADESESGNSSE---LGKEFFCSYKDLIDRG--- 171 + P+ PR ++F+ E G S + S ++ +R Sbjct: 130 MIPELKTQPRGQLRCSSLPHLKRVMFLGAEKHRGMYSVPEIISMSAMVSDEEYAERQRAL 189 Query: 172 DPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCH-----RGIFIMTVDSLIDWGVPKQP 226 DP D + + YTSGTT PKGV+ H G +I + K Sbjct: 190 DPH----------DVVNMQYTSGTTGFPKGVMLTHVNIGNNGYWIGKNQHFTE----KDR 235 Query: 227 VYLWTLPMFHANGWSYPWGMAAV--GGTNICLRKFDSEIIYDMIKRHGVTHMCGAP---- 280 V L +P+FH G +AA+ G + L F + + + T + G P Sbjct: 236 VCL-PVPLFHCFGCVLGV-LAAINHGAALVILESFSPMHVMASVDQEKCTALYGVPTMFL 293 Query: 281 -VVLNMLSNAPGSEPLKTTVQIMTAGAPPPSAVLFRTESLGFA--VSHGYGLTETAGLVV 337 V+ + L L+T + AG+ P ++ R + ++ YGLTE + ++ Sbjct: 294 AVLEHKLFERFDFSSLRTGIM---AGSVCPEPLMRRVVEKMYMREITICYGLTEGSPVMT 350 Query: 338 SCAWKKEWNHLPATERARLKSRQGVGTVMQT-KIDVVDPVTGAAVKRDGSTLGEVVLRGG 396 + + Q VG M ++ +VDP T V R T GEVV RG Sbjct: 351 QSLVTDPFE----------RRVQTVGRAMPCIEVRIVDPDTNEEVPR--GTQGEVVCRGY 398 Query: 397 SVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVE 456 +VM GY PE T ++ ADGW ++GD+GVM +GY+ I R KD+II GGEN+ E+E Sbjct: 399 NVMKGYYNMPEATTAAIDADGWLHSGDLGVMDEEGYVVITGRIKDMIIRGGENIYPREIE 458 Query: 457 SILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPK 516 LY + + VV +GE AF+ K G+ P +++ +YCR ++ + VP+ Sbjct: 459 EFLYGMDGVQDVQVVGVNSRKYGEEVGAFIIPKPGVEMAP--EDVRDYCRGRIAWHKVPR 516 Query: 517 TVVFKEELPKTSTGKVQKFILRDMA 541 + F + P T++GK+QKF LR+MA Sbjct: 517 YISFIDAYPMTASGKIQKFKLREMA 541 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: 703 Number of extensions: 36 Number of successful extensions: 4 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: 550 Length adjustment: 36 Effective length of query: 520 Effective length of database: 514 Effective search space: 267280 Effective search space used: 267280 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