Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_085972625.1 BBTA_RS20515 acyl-CoA synthetase
Query= BRENDA::O74725 (578 letters) >NCBI__GCF_000015165.1:WP_085972625.1 Length = 544 Score = 129 bits (325), Expect = 2e-34 Identities = 142/538 (26%), Positives = 238/538 (44%), Gaps = 65/538 (12%) Query: 49 KSYSSKEVANRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTIDSLPLFWAVHRLGGV 108 +S++ +E+ V +LA +L+++ G + V + N + +A RLG V Sbjct: 48 RSWTWRELDAMVSALAAALAEQ-------GIVKGDRILVHSKNCEEMFVSMFAAFRLGAV 100 Query: 109 LTPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLPKNRIYLLDVPEQLLG 168 P N E+ + S AKA + P++ + Sbjct: 101 WVPTNFRLMPDEVAYLATASGAKAFL-------------CHGDFPEHAAAVTTTDFTWRI 147 Query: 169 GVKPPAGYKSVSELTQAGKSLPPVDELRWSAGEGARRTAFVCYSSGTSGLPKGVMISHRN 228 G G ++V+E +A E+ +A E F ++SGT+G K +++H Sbjct: 148 GEGGSLGTRAVAEAIRAHAGA----EIANAAVEHDDPCWFF-FTSGTTGRSKAAVLTHGQ 202 Query: 229 ---VIANTLQIKAFEQNYRDGGGTKPASTE--VALGLLPQSHIYALVVIGHAGAYRGDQT 283 VI N L P +TE +L + P SH + + + RG +T Sbjct: 203 MAFVITNHL------------ADLTPGTTEHDASLVVAPLSHGAGVHQLMQSA--RGAKT 248 Query: 284 IVLP--KFELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYDLSSVTSLFTGAAPL 341 ++LP KF++ + I+++++S LF VP I+ M+ ++D SS+ + AP+ Sbjct: 249 VLLPSEKFDIAEAFSLIERHRVSNLFTVPTIL-KMMVEHPAIDQFDHSSLRHVIYAGAPM 307 Query: 342 GMETAADFLKLYPNILIRQGYGLTETC----TVVSSTHPHD----IWLGSSGALLPGVEA 393 E L +++ Q +GL E + ++ H + +G+ G G++ Sbjct: 308 YREDQKRALARLGKVIV-QYFGLGEVTGNITVLPAAAHEEEDGPEARIGTCGYERTGMQV 366 Query: 394 RIVTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFVDGWMRTGDEAVIRRSPKG 453 I + +E+ ++ GE+ V P+V GY +N +A A+ F DGW RTGD + +G Sbjct: 367 SIQDDQGRELKPSET-GEICVIGPAVFAGYYDNPEANAKAFRDGWFRTGD--LGHMDAQG 423 Query: 454 IEHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVPKAIVVKS 513 V+I R ++ G + P E+E IL HP + + AV+ +PD GEV A+ V Sbjct: 424 F--VYITGRASDMYISGGSNIYPREVEEKILTHPAIGEVAVLGVPDPVWGEVGVAVCV-- 479 Query: 514 ASAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIRDQEKEAR 571 A G + Y+ R+K K F DA+PKS GKI +RL+RD E EAR Sbjct: 480 AREGGAAPSESEIAGYLATKLPRYKMPK-RFFFWDALPKSGYGKIPKRLVRD-ELEAR 535 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: 715 Number of extensions: 41 Number of successful extensions: 4 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: 544 Length adjustment: 36 Effective length of query: 542 Effective length of database: 508 Effective search space: 275336 Effective search space used: 275336 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 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