Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate Pf6N2E2_1879 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= BRENDA::O74725 (578 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1879 Length = 511 Score = 163 bits (413), Expect = 1e-44 Identities = 147/524 (28%), Positives = 257/524 (49%), Gaps = 52/524 (9%) Query: 48 GKSYSSKEVANRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTIDSLPLFWAVHRLGG 107 GK +S ++ + LA SL + G + + +++++ N+ + + ++A+ ++G Sbjct: 26 GKYWSFLDIDVQSSRLAASLE-------SMGVKREDVVSIYSPNSPEWIITYYAILKIGA 78 Query: 108 VLTPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLPKNRIYLLDVPEQLL 167 ++ P N +A E + + A A+ + S L A + P I L+ + Sbjct: 79 IVNPLNTMLTAREAAFAIKNCGAVAVFST----SDKLLALQEHIGPTEVISLISFDGITV 134 Query: 168 GGVKPPAGYKSVSELTQAGKSLPPVDELRWSAGEGARRTAFVCYSSGTSGLPKGVMISHR 227 G++ + + + A + P G + + Y+SGT+G PKG ++SHR Sbjct: 135 AGMRH---FNLLVDANVAVREYPVT-------GIQKDDISTIGYTSGTTGQPKGAVLSHR 184 Query: 228 NVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQSHIYALVVIGHAGAYRGDQTIVLP 287 ++ N ++++A+ LP SH+Y VV+ A AY T+VL Sbjct: 185 CILTNVSMTATMHLR---------TASDIAVSALPLSHVYGNVVMNSAIAY--GMTLVLH 233 Query: 288 K-FELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYDLSSVTSLFTGAAPLGMETA 346 K F+ ++ L++IQ Y + L VP + I++L ++ YD+SS+T G + TA Sbjct: 234 KTFDAEAILSSIQIYGATLLEGVPTMYIYLLNCPNL-GAYDVSSLTRCTVGGQMMPY-TA 291 Query: 347 ADFLKLYPNILIRQGYGLTETCTVVSSTHPHDIW----LGSSGALLPGVEARIVTPE-NK 401 + ++ + + +G+TE + ++ H ++ LGS G LP +EARI E + Sbjct: 292 MENVERALGCRLLELWGMTELGGLGTT---HSLYGERRLGSIGVALPHLEARIAQLELDG 348 Query: 402 EITTYDSPGELVVRSPSVVLGYLNNEKATAETFVD-GWMRTGDEAVIRRSPKGIEHVFIV 460 + GEL +R P V+ YL ATAET D GW+RTGD A R +G ++IV Sbjct: 349 DALPLGEIGELQIRGPVVMKHYLGRPDATAETKTDEGWLRTGDLA--RMDSEGF--IYIV 404 Query: 461 DRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVPKAIVVKSASAGSDE 520 DR+K++ G + PAELE I HP V+ AV ++ D+ GE+ KA +V D Sbjct: 405 DRLKDMFITAGFNIYPAELERVIAEHPSVAMVAVGSVLDEIKGELAKAYIVPKTGYEID- 463 Query: 521 SVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIR 564 Q + ++ D A +K + + V+ +PK+ SGK++RR++R Sbjct: 464 --IQQIERHCRDRLAAYK-VPRLFQIVEDLPKTSSGKVMRRMLR 504 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: 573 Number of extensions: 29 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 578 Length of database: 511 Length adjustment: 35 Effective length of query: 543 Effective length of database: 476 Effective search space: 258468 Effective search space used: 258468 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 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