Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate H281DRAFT_05129 H281DRAFT_05129 long-chain acyl-CoA synthetase
Query= BRENDA::O74725 (578 letters) >FitnessBrowser__Burk376:H281DRAFT_05129 Length = 610 Score = 171 bits (432), Expect = 1e-46 Identities = 155/548 (28%), Positives = 242/548 (44%), Gaps = 45/548 (8%) Query: 50 SYSSKEVANRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTIDSLPLFWAVHRLGGVL 109 +Y S + L R + + + G + +A+ NT + V + G V+ Sbjct: 85 AYVSVGASMTYGELGRKATAFAAYLQSIGVKPGARVAIMLPNTFQYPVSLFGVLKAGAVV 144 Query: 110 TPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLPKNRIYLLDVPEQLLGG 169 N Y+ EL HQL DS A+ ++ +A G + + + + L G Sbjct: 145 VNVNPLYTVRELAHQLKDSGAQTIIVFENFAKTVQDALP--GSKVQNVIVTGLGDLLADG 202 Query: 170 VKPPAGY-----KSVSELTQAGKSLPPVDELRWSAGEGARRT-----------AFVCYSS 213 + + V ++ A SLP L + G R AF+ Y+ Sbjct: 203 LNLKGRVLNFMLRHVKKMVPA-YSLPNAVPLLKALAIGYTRPLTPVRPTHHDIAFLQYTG 261 Query: 214 GTSGLPKGVMISHRNVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQSHIYALVVIG 273 GT+G+ KG M++HRN+IAN LQ KA+ + G E L LP HIY+L V Sbjct: 262 GTTGVAKGAMLTHRNIIANLLQAKAWAEGQLSG------EVETVLTPLPLYHIYSLTVNA 315 Query: 274 HAGAYRGDQTIVLPK-FELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYDLSSVT 332 G + I++ ++K + I+ K + + V + L ++ C K D S + Sbjct: 316 LIFMGLGGRNILIANPRDMKRVMMIIRHEKFTGMTAVNTLYNAFLENEEFC-KRDFSDLK 374 Query: 333 SLFTGAAPLGMETAADFLKLYPNILIRQGYGLTETCTVVSSTHPHDI-----WLGSSGAL 387 G A F + +I +GYGLTE C+ + S +P DI + GS G Sbjct: 375 LAMAGGMATQRSVAERFKAVTGKPII-EGYGLTE-CSPIVSMNPVDISNLRDFEGSIGLP 432 Query: 388 LPGVEARIVTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFVD-GWMRTGDEAV 446 P + R ++ GEL V+ P V+ GY N + TA+ D GW+ TGD V Sbjct: 433 APSTQVRF-RKDDGSWANIGEAGELCVKGPQVMKGYWNRPEETAKVIDDEGWLATGDIGV 491 Query: 447 IRRSPKGIEHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVP 506 + +G + ++DR K++I V G V P E+E I AHPDV + A I +PDD GE Sbjct: 492 M--DSRGF--IRLIDRKKDMILVSGFNVYPNEIEDVIAAHPDVREVAAIGVPDDAQGERV 547 Query: 507 KAIVVKSASAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIRDQ 566 K +VK + + E V K + +K + + F D +P++ GKILRR +RD+ Sbjct: 548 KVFIVKRNPSLTAEQVIAHCRKNLTGYK-----VPKVVEFRDELPQTNVGKILRRALRDE 602 Query: 567 EKEARRKA 574 E ++ A Sbjct: 603 ELAKQKTA 610 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: 753 Number of extensions: 36 Number of successful extensions: 6 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: 610 Length adjustment: 37 Effective length of query: 541 Effective length of database: 573 Effective search space: 309993 Effective search space used: 309993 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