Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_106709349.1 CU102_RS02485 acyl--CoA ligase
Query= BRENDA::O74725 (578 letters) >NCBI__GCF_003010955.1:WP_106709349.1 Length = 512 Score = 148 bits (374), Expect = 5e-40 Identities = 144/533 (27%), Positives = 250/533 (46%), Gaps = 58/533 (10%) Query: 48 GKSYSSKEVANRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTIDSLPLFWAVHRLGG 107 G+ + E+ + D LA +L W+ +G + VF N ++ +A+ + G Sbjct: 24 GERLTYAELDDLSDRLAAAL-----WS--QGVTRGDRVLVFMNNCWEATVAIYAILKAGA 76 Query: 108 VLTPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLPKNRIYLLDVPEQLL 167 V +P NAS A +L + + + +A+A++ L +++EA G + ++ + L Sbjct: 77 VFSPINASTKADKLAYIIENCRARAIIAQEKLAPVAVEAM---GDRTSCDLIVTTKNETL 133 Query: 168 GGVKPPAGYKSVSELTQAGKSLPPVDELRWSAGEGARRTAFVCYSSGTSGLPKGVMISHR 227 + ++ SL V+ + G A + Y+SG++G PKGVM++HR Sbjct: 134 A-----------APYARSFDSLLQVEPMPVPHGGIDVDLAMLIYTSGSTGRPKGVMMNHR 182 Query: 228 NVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQSHIYALVVIGHAGAYRGDQTIVLP 287 N+ A I + QN D ++ L +LP + Y L + R T+VL Sbjct: 183 NIEAAATSITTYVQNVED---------DIILNVLPLAFDYGLYQLFMT--IRTGATLVLE 231 Query: 288 -KFEL-KSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKY--DLSSVTSLFTGAAPLGM 343 F ++ + +++ ++ LVP + +L +D+ + DL +T+ AA L Sbjct: 232 TSFSFPQAIFDVMRREHVTGFPLVPTMAALILQMRDIEPGFLPDLRYITNT---AAALPP 288 Query: 344 ETAADFLKLYPNILIRQGYGLTET--CTVVSSTHPHDIWLGSSGALLPGVEARIVTPENK 401 A +L+P + + YGLTE CT + D GS G +P E +V E K Sbjct: 289 AHIARLRELFPGVRLYSMYGLTECKRCTYLPPQQL-DHRPGSVGIAIPNTETFVVDDEGK 347 Query: 402 EITTYDSPGELVVRSPSVVLGYLNNEKATAETFVDG---WMR---TGDEAVIRRSPKGIE 455 + GELV+R P V+ GY N++ATA G W + TGD S G Sbjct: 348 AVAP-GVVGELVIRGPHVMQGYWENDEATARMLRPGLNPWEKVLYTGDLF----SMDGDG 402 Query: 456 HVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVPKAIVVKSAS 515 +++ V R ++IK +G +VAP E+E + +HP +++ VI IPD G+ +AIVV S Sbjct: 403 YLYFVGRKDDIIKTRGEKVAPKEVETVLHSHPGIAEAVVIGIPDPVLGQAIRAIVVLSDP 462 Query: 516 AGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIRDQEK 568 + +D + + K +ED + + F ++PK+ +GK+ RRL + ++ Sbjct: 463 SLTDREIIRHCSKNLEDF-----MVPKSVEFRTSLPKTDTGKVSRRLAAEPQE 510 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: 641 Number of extensions: 28 Number of successful extensions: 5 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: 512 Length adjustment: 35 Effective length of query: 543 Effective length of database: 477 Effective search space: 259011 Effective search space used: 259011 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