Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_072791060.1 BUA36_RS29590 long-chain-fatty-acid--CoA ligase
Query= metacyc::MONOMER-20125 (556 letters) >NCBI__GCF_900143065.1:WP_072791060.1 Length = 563 Score = 163 bits (413), Expect = 1e-44 Identities = 160/562 (28%), Positives = 240/562 (42%), Gaps = 71/562 (12%) Query: 20 LERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYE 79 LE + Y + + V T+++ L + + S G++ G V+++ PNV Q Sbjct: 29 LEESFHKYANRNAYVCMDKFLTYAEVDAYSKRLGAWLQSRGLKPGARVAIMMPNVLQYPI 88 Query: 80 LHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQA--- 136 A+ AG + VN R + L+ S S+ I +ILE A +Q Sbjct: 89 AIAAILRAGYTVVNVNPLYTPRELEHQLNDSGSEAI--------IILENFATTLEQVLGR 140 Query: 137 -PVPRLVFMADESESGNSSELGKEFFCS----------------YKDLIDRGDPDFKWVM 179 V +V + G + F +KD + +G + Sbjct: 141 TQVKHIVVASMGEMLGGLKGMLVNFVVRSVKKMVPAFSLPNAVRFKDALSQGGGMKLTPV 200 Query: 180 PKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVP------KQPVYLWTLP 233 + DP L YT GTT KG H+ I + S W P +Q + LP Sbjct: 201 ERQYNDPAFLQYTGGTTGVSKGATLTHQNIVANLLQSEA-WSQPALGGSDEQVTIVCALP 259 Query: 234 MFHANGWSY--PWGMAAVGGTNICL-RKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP 290 ++H + WG VG NI + D + ++ + + N L N P Sbjct: 260 LYHIFALTACAMWG-TRVGALNILIPNPRDIGGFIKELAKYKFNMLPAVNTLYNALLNHP 318 Query: 291 GSEPLK-TTVQIMTAGAPP-PSAVLFR-TESLGFAVSHGYGLTETAGLVVSCAWKKEWNH 347 L + ++I G AV R ++ G ++ GYGL+ET+ Sbjct: 319 DFVHLDFSALKICNGGGMAVQQAVNDRWLKATGVSIIEGYGLSETS-------------- 364 Query: 348 LPATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGS------TLGEVVLRGGSVMLG 401 P R S GT I + P T A+ D T GE+ +RG VM G Sbjct: 365 -PVATCNRADSTAFTGT-----IGLPVPSTDIAILDDDGNEVALGTAGEIAIRGPQVMAG 418 Query: 402 YLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYS 461 Y P+ TAK MT DG+F +GDVGVM GY++I DR KD+I+ G N+ E+E ++ + Sbjct: 419 YWNRPDETAKVMTPDGFFKSGDVGVMDASGYVKIVDRKKDMILVSGFNVYPNELEGVIAA 478 Query: 462 HPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFK 521 HP +LE A + PD++ GE FV K TE E++ YC+ +L Y PK + F+ Sbjct: 479 HPGVLECAAIGVPDDYSGEAVKVFVVRK---DPNLTEAELMAYCKEQLTGYKKPKYIEFR 535 Query: 522 EELPKTSTGKVQKFILRDMARG 543 EELPKT+ GK+ + +LRD A G Sbjct: 536 EELPKTNVGKILRRMLRDEAPG 557 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: 31 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: 563 Length adjustment: 36 Effective length of query: 520 Effective length of database: 527 Effective search space: 274040 Effective search space used: 274040 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