Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF2497 PGA1_c25300 long-chain-fatty-acid--CoA ligase FadD
Query= BRENDA::O74725 (578 letters) >FitnessBrowser__Phaeo:GFF2497 Length = 577 Score = 142 bits (359), Expect = 3e-38 Identities = 147/539 (27%), Positives = 243/539 (45%), Gaps = 55/539 (10%) Query: 49 KSYSSKEVANRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTIDSLPLFWAVHRLGGV 108 K+Y+ E+ D++A L ++ G P + A+ N+I + + + G Sbjct: 71 KTYA--EIGRASDAIACYLREDLGLFPGD------VAAIQLPNSIHYPVILFGAMKAGLK 122 Query: 109 LTPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLPKNRIYLLDVPEQLLG 168 +T N Y+ E+ HQL DS AK L L + L+ A + + + L Sbjct: 123 VTNLNPLYTPREIVHQLQDSGAKVLFG-FNLFADRLQTALRDTAVEQVVIAA------LW 175 Query: 169 GVKPPAGYKSVSE-LTQAGKSLPPVD-----------------ELRWSAGE-GARRTAFV 209 P A ++ +T K +P E+ + + AF+ Sbjct: 176 EFFPQAASDALRHTITDVAKLVPEYSFDHVPFEDAFAQGMAHGEIHYDLSQIDPGSAAFL 235 Query: 210 CYSSGTSGLPKGVMISHRNVIANTLQIKAFEQNYRDGGGTKPASTEVA-LGLLPQSHIYA 268 Y+ GT+G+ KG ++H NV + A G K +++ L ++P HI+A Sbjct: 236 QYTGGTTGVSKGAELTHDNVTHVLEMLNACVH----GAMQKTDHGQMSILTVIPYYHIFA 291 Query: 269 LVV-IGHAGAYRGDQTIVLPKFELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYD 327 L+V + H A G ++ + + A Y I L V + ++ QD + Sbjct: 292 LIVNLMHFTAASGRNVLIPNPNPIANLKPAFDNYDIDWLTGVDTLFNGLMA-QDWFQQTP 350 Query: 328 LSSVTSLFTGAAPLGMETAADFLKLYPNILIRQGYGLTET-CTVVSSTHPHDIWLGSSGA 386 + G L +TA + + I+ +GYG+TET C + S G++G Sbjct: 351 -PQIGLAIGGGTSLRPDTARRWSEQIGPIV--EGYGMTETTCMIALSPLDGSDKPGTAGQ 407 Query: 387 LLPGVEARIVTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFVDGWMRTGDEAV 446 +PG+E +I + + ++ GEL VR P++ YLN A+AETF DGWM TGD + Sbjct: 408 PVPGLEIKITRSDGAPVGIGEA-GELHVRGPNIATAYLNRPDASAETFADGWMATGD--I 464 Query: 447 IRRSPKGIEHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVP 506 + +G H+ IVDR K++I V G V P ELEA I + P V++ AV+ GE P Sbjct: 465 VTMDAEG--HLAIVDRKKDMILVSGFNVYPNELEAVIQSMPGVAEVAVVGEAHPTRGESP 522 Query: 507 KAIVVKSASAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIRD 565 A V ++ A ++E V +KY + +K + + F++ +PKS GKILR+ +R+ Sbjct: 523 AAFVKRADPAVTEEMV----IKYCRANLTAYK-VPTQVHFLEELPKSSVGKILRKELRN 576 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: 721 Number of extensions: 40 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: 577 Length adjustment: 36 Effective length of query: 542 Effective length of database: 541 Effective search space: 293222 Effective search space used: 293222 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