Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate Ac3H11_1843 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= BRENDA::O74725 (578 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1843 Length = 560 Score = 155 bits (391), Expect = 5e-42 Identities = 149/500 (29%), Positives = 232/500 (46%), Gaps = 69/500 (13%) Query: 101 AVHRLGGVLTPANASYSAAELTHQLLDSKAKALVTCV----PLLSISLEAAAKAGLPKNR 156 AV R G N Y+A EL HQL DS A A+V L + A K + + Sbjct: 92 AVLRAGYTCVNVNPLYTARELEHQLKDSGATAIVILENFAHTLADVIDHTAVKHVVMASM 151 Query: 157 IYLL----------------------DVPEQLLGGVKPPAGYKSVSELTQAGKSLPPVDE 194 LL D+P L GG K K++S KSL P Sbjct: 152 GDLLGFWFGQWITFAVRHLAKMVPAYDLP--LTGGRKVVTFKKALS--VGEHKSLAPSQA 207 Query: 195 LRWSAGEGARRTAFVCYSSGTSGLPKGVMISHRNVIANTLQIKAFEQNYRDGGGTKPAST 254 S AF+ Y+ GT+GL KG +++HRN++A TLQ +A+ G + Sbjct: 208 TLDSI-------AFLQYTGGTTGLSKGAVLTHRNIVAATLQAEAWFTPALSKVGDLSKAN 260 Query: 255 EVALGLLPQSHIYALVVIGHAGAYRGDQTIV-----LPKFELKSYLNAIQQYKISALFLV 309 +A LP HI+AL + A T++ +PKF + + K ++ Sbjct: 261 SIAA--LPLYHIFALTLCLLAIRQGSSLTLIPNPRDIPKF--------VAELKKRPFHML 310 Query: 310 PPI--IIHMLGTQDVCSKYDLSSVTSLFTGAAPLGMETAADFLKLYPNILIRQGYGLTET 367 P + + + L D S + G TA + K+ + +I +G+G++ET Sbjct: 311 PAVNTLFNALLQNPQFKTLDFSHLCVSQAGGMAASEGTAKQWQKVTGSTMI-EGWGMSET 369 Query: 368 CTVVSSTHP--HDIWLGSSGALLPGVEARIVTPENKEITTYDSPGELVVRSPSVVLGYLN 425 C + + +P + G+ G LPG++ I + + +S GE+ +R P+V++GY N Sbjct: 370 CAI-GTNNPVISTTFSGNIGLPLPGIDIAIKDDDGNSLPQGES-GEICIRGPNVMVGYYN 427 Query: 426 NEKATAETFV-DGWMRTGDEAVIRRSPKGIEHVFIVDRIKELIKVKGLQVAPAELEAHIL 484 + A+ F DG+MRTGD ++ P+G + I+DR K++I V G V P ELE I Sbjct: 428 QPEENAKAFTPDGFMRTGDIGIM--DPQG--YTRIIDRKKDMILVSGFNVFPNELEQVIS 483 Query: 485 AHPDVSDCAVIAIPDDRAGEVPKAIVVKSASAGSDESVSQALVKYVEDHKARHKWLKGGI 544 P V +CA I +PD++ GE K ++K+ A +++ V+ + + +K R K+ I Sbjct: 484 LCPGVVECAAIGVPDEKQGEAIKVFIIKNDPALTEDEVANYCHQNLTGYK-RPKY----I 538 Query: 545 RFVDAIPKSPSGKILRRLIR 564 F D +PKS GKILRR +R Sbjct: 539 EFRDELPKSNVGKILRRELR 558 Lambda K H 0.316 0.134 0.392 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: 784 Number of extensions: 47 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 578 Length of database: 560 Length adjustment: 36 Effective length of query: 542 Effective length of database: 524 Effective search space: 284008 Effective search space used: 284008 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: 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