Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate RR42_RS18150 RR42_RS18150 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__Cup4G11:RR42_RS18150 Length = 560 Score = 205 bits (522), Expect = 3e-57 Identities = 179/578 (30%), Positives = 264/578 (45%), Gaps = 54/578 (9%) Query: 6 NYPLVDIPEVDLWTF-----LFERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKG 60 +YP E+D F L E R Y D + + TY L S F Sbjct: 8 HYPAGVPAEIDSSQFHSLAELLEASFRTYADRRAF---VCMDKSITYGELDRMSRQFAAW 64 Query: 61 LKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKG 120 L++ + G +A+ PN + PVV+ L AG + NP YT EL QLK+S A+ Sbjct: 65 LQSR-GLKPGARVAIMMPNVLQYPVVLAAVLRAGFVVVNVNPLYTPRELEHQLKDSGAEA 123 Query: 121 LV-------TQASVLPVAREAAKKVGMPEDRIILIGDQRDPDAR-----VKHFTSVRNIS 168 +V T VLP V D L+G + VK + Sbjct: 124 IVILENFATTLQQVLPATPVKHVVVASMGD---LLGGLKGAIVNFVVRNVKKMVPAWELP 180 Query: 169 GATRY-------RKQKITPAK----DVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIA 217 R+ R ++ PA DVAFL Y+ GTTGV KG ++ HRNIV+N+ Q Sbjct: 181 NCVRFNAVLAEGRGMQLQPATTGPDDVAFLQYTGGTTGVSKGAVLLHRNIVSNVLQSEAW 240 Query: 218 EGEMLSWNGGPDGKGDRVLAFLPFYHIYGLT-CLITQALYKGYHLIVMSKFDIEKWCAHV 276 L+ G P + + A LP YHI+ LT C + G +++ + DI + + Sbjct: 241 MQPALA-KGAPIDQVITITA-LPLYHIFALTVCCLLGMRSGGLSVLIPNPRDIPGFIKEL 298 Query: 277 QNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQ 336 Q Y+ + V + L P +DK D S LR+ N G + + + + +R I + Sbjct: 299 QKYKFNMFPAVNTLYNALINSPDIDKVDFSGLRVANGGGMAVQEAVAKKWLARTGCPIIE 358 Query: 337 GYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYL 396 GYGLSETSP+ D G++G +P+ +DG++ V G+ GE+ + Sbjct: 359 GYGLSETSPSATCNP-TDSDAFSGTIGLPLPSTDIAIRD--DDGAD---VPLGQAGEICI 412 Query: 397 KGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPA 456 +GP V GY P+ T ++ DG+F++GD+G DA+G I DR K++I GF V P Sbjct: 413 RGPQVMAGYWNRPDETAKVMTADGFFKSGDIGVMDARGYTKIVDRKKDMILVSGFNVYPN 472 Query: 457 ELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDS 516 E+EG + + +VA +G+ E H EV VVR K +E A +I + Sbjct: 473 EVEGVAAECPGVLEVAAVGVPDE-HSGEVVKLYVVR----KDPALTE----AELIAFCKE 523 Query: 517 KVASHKRLRGGVHFVDEIPKNPSGKILRRILKQKFKGA 554 ++ +KR + V F E+PK GKILRR L+ K A Sbjct: 524 RLTGYKRPK-FVEFRSELPKTNVGKILRRELRDSRKAA 560 Lambda K H 0.317 0.136 0.410 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: 720 Number of extensions: 36 Number of successful extensions: 6 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: 562 Length of database: 560 Length adjustment: 36 Effective length of query: 526 Effective length of database: 524 Effective search space: 275624 Effective search space used: 275624 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 (21.7 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