Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_028310635.1 H566_RS0105380 malonyl-CoA synthase
Query= BRENDA::O74725 (578 letters) >NCBI__GCF_000482785.1:WP_028310635.1 Length = 518 Score = 149 bits (375), Expect = 4e-40 Identities = 135/486 (27%), Positives = 226/486 (46%), Gaps = 36/486 (7%) Query: 85 LAVFALNTIDSLPLFWAVHRLGGVLTPANASYSAAELTHQLLDSKAKALVTCVPLLSISL 144 LA ++++L L+ A R G V P N +Y AE+ + + D+K A+V C P + Sbjct: 59 LAAQVDKSVEALMLYLACLRAGIVYVPLNTAYRKAEVEYFIGDAKP-AVVVCTPA---NF 114 Query: 145 EAAAKAGLPKNRIYLLDVPEQLLGGVKPPAGYKSVSELTQAGKSLPPVDELRWSAGEGAR 204 KA + + + G + A + + +T Sbjct: 115 SWVGKAAFCGGAEVVYTLGDDRGGTLLDRAAHHADDFVT---------------VDRADA 159 Query: 205 RTAFVCYSSGTSGLPKGVMISHRNVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQS 264 A + Y+SGT+G KG M+SH N+ +N L +++ + GT PA + L LP Sbjct: 160 DLAVLLYTSGTTGRSKGAMLSHGNMASNALALRSLWGWHLAPDGT-PAERDTLLHALPLF 218 Query: 265 HIYALVVIGHAGAYRGDQTIVLPKFELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCS 324 HI+ L V H G + I LP+ + + L+ + + + + VP + +L + Sbjct: 219 HIHGLFVAAHGALIAGAKQIFLPRLDPAAILDLLP--RCTVMMGVPTYYVRLLAEPGLTP 276 Query: 325 KYDLSSVTSLFTGAAPLGMETAADFLKLYPNILIRQGYGLTETCTVVSSTHPHDIWL--- 381 + + + +G+APL ET + + ++++ + YG++ET S+ + D L Sbjct: 277 ER-CAGMRLFVSGSAPLLKETFELWRERTGHVILER-YGMSETVMNTSNPYDGDPALRKP 334 Query: 382 GSSGALLPGVEARIVTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFV-DGWMR 440 G+ G +PGV R+V + G++ + P+V GY TAE+F DGW R Sbjct: 335 GTVGPAIPGVGVRVVDGRTDQPLPAGEIGDIQISGPNVFGGYWQMPDKTAESFTADGWFR 394 Query: 441 TGDEAVIRRSPKGIEHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDD 500 TGD V R G ++ IV R K+LI G V P E+E+ I P V++ AVI +P Sbjct: 395 TGD--VGRLDDDG--YLSIVGRSKDLIITGGYNVYPKEIESFIDEMPGVAESAVIGVPHA 450 Query: 501 RAGEVPKAIVVKSASAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILR 560 GE A+VV A DE+ AL+ ++ A +K K + VD +P++ GK+ + Sbjct: 451 DFGEAVVAVVVPRPDAVVDEA---ALIAALKAGIANYKVPK-RVFTVDELPRNTMGKVQK 506 Query: 561 RLIRDQ 566 L+R++ Sbjct: 507 NLLRER 512 Score = 25.0 bits (53), Expect = 0.008 Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 3/64 (4%) Query: 42 YTCGITGKSYSSKEVANRVDSLARSLSKEFGW--APNEGSEWDKTLAVFALNTIDSLPLF 99 YT G TG+S + + S A +L +GW AP +G+ ++ + AL LF Sbjct: 166 YTSGTTGRSKGAMLSHGNMASNALALRSLWGWHLAP-DGTPAERDTLLHALPLFHIHGLF 224 Query: 100 WAVH 103 A H Sbjct: 225 VAAH 228 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: 700 Number of extensions: 47 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 578 Length of database: 518 Length adjustment: 36 Effective length of query: 542 Effective length of database: 482 Effective search space: 261244 Effective search space used: 261244 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