Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_017599838.1 D471_RS0117595 hypothetical protein
Query= BRENDA::O74725 (578 letters) >NCBI__GCF_000341125.1:WP_017599838.1 Length = 505 Score = 164 bits (416), Expect = 6e-45 Identities = 164/535 (30%), Positives = 239/535 (44%), Gaps = 51/535 (9%) Query: 34 RHASSRDPYTCGITG-KSYSSKEVANRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNT 92 R A S T + G +S++ E+ RV LA +L G G +A N Sbjct: 12 RRARSCPERTALVHGERSFTYAELHERVTRLAAALR---GLGVRRGDR----VAYLGANH 64 Query: 93 IDSLPLFWAVHRLGGVLTPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGL 152 + +A LG V P N + EL + + DS + CV L+ + +A A GL Sbjct: 65 PALVETLFAAGTLGAVFVPLNTRLAVPELAYAIEDSGS-----CV-LVHGAEQAEAAGGL 118 Query: 153 PKNRIYLLDVPEQLLGGVKPPAGYKSVSELTQAGKSLPPVDELRWSAGEGARRTAFVCYS 212 + VP P GY+++ + A PVDE G T + Y+ Sbjct: 119 RDRTAPRVLVPVD----DDAPDGYEALIASSPAA----PVDE-----PVGLDDTCMIMYT 165 Query: 213 SGTSGLPKGVMISHRNVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQSHIYALVVI 272 SGT+G PKG ++H N+ N + + D EV L P H AL + Sbjct: 166 SGTTGHPKGAELTHGNITWNCVNVLIDVDVTVD---------EVTLVTAPLFHTAALNMT 216 Query: 273 GHAGAYRGDQTIVLPKFELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYDLSSVT 332 +G + IV P F+ + ++S +F VP + L + DLSS+ Sbjct: 217 CLPTLLKGGRVIVEPGFDPTRVIELFTARRVSWMFGVPAMF-DALAAHPGWAGADLSSLR 275 Query: 333 SLFTGAAPLGMETAADFLKLYPNILIRQGYGLTETCTVVSSTHPHDIWLGSSGALLPGV- 391 L G AP+ T A + K + QGYG+TET V D + A P V Sbjct: 276 VLMAGGAPVPESTIAAYQKR--GLTFLQGYGMTETAPGVLMLGAADSLRKAGTAGRPSVF 333 Query: 392 -EARIVTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFV-DGWMRTGDEAVIRR 449 + RIV P+ + + PGE+VV+ P+V+ GY TA DGW RTGD A + Sbjct: 334 TDVRIVRPDLTDAAPGE-PGEIVVKGPNVMRGYWGRPDDTARAHTADGWFRTGDVATV-- 390 Query: 450 SPKGIEHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVPKAI 509 +G V IVDR K++I G V PAE+E + HPDV +CAVI +PD+R GEV +A+ Sbjct: 391 DAEGF--VRIVDRAKDMIISGGENVYPAEVENVLHDHPDVLECAVIGVPDERWGEVGRAV 448 Query: 510 VVKSASAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIR 564 VV E L+ + E AR+K K + F D +P++ +GK+ + +R Sbjct: 449 VVPRPGTAPAEG---DLLAHFEGRLARYKTPK-SVVFTDELPRNAAGKLRKADLR 499 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: 738 Number of extensions: 39 Number of successful extensions: 6 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: 578 Length of database: 505 Length adjustment: 35 Effective length of query: 543 Effective length of database: 470 Effective search space: 255210 Effective search space used: 255210 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: 52 (24.6 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