Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate HSERO_RS19285 HSERO_RS19285 long-chain fatty acid--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__HerbieS:HSERO_RS19285 Length = 566 Score = 182 bits (461), Expect = 4e-50 Identities = 155/549 (28%), Positives = 252/549 (45%), Gaps = 52/549 (9%) Query: 32 DKIIYQDADTQ------RHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPV 85 D+ Q AD Q ++ +Y+ L S G L+ L +KG +A+ PN + P+ Sbjct: 30 DEAFVQHADRQAYVCMGKYLSYRELDSLSRALGGWLQGL-GLQKGARVAIMMPNVLQYPI 88 Query: 86 VMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRI 145 + L AG T+ NP YT EL QLK+S A+ + + ++ + + Sbjct: 89 AIAAILRAGYTVVNVNPLYTARELEHQLKDSGAEAIFVLENFACTLQKVVAHTNIKHIVV 148 Query: 146 ILIGDQRDP------DARVKH-------------FTSVRNISGATRYRKQKITPAKD-VA 185 +G+ + V+H T + +S A Q +T D +A Sbjct: 149 ASMGELLGALKGTLVNLVVRHVKKLVPAWSLPNAITFSQALSQARGKTLQPVTLTHDDIA 208 Query: 186 FLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAF---LPFY 242 FL Y+ GTTGV KG +++HRN+VAN+ Q E GK L F LP Y Sbjct: 209 FLQYTGGTTGVAKGAVLTHRNLVANVLQ-----AEEWLTPALKAGKPIDQLVFVCALPLY 263 Query: 243 HIYGLT-CLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVD 301 HI+ LT C + +L++ + DI + + Y+ + V + L + Sbjct: 264 HIFALTVCNMLGTREGALNLLIPNPRDIPGFVKELAKYKVNTFPAVNTLYNALLNNADFA 323 Query: 302 KYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGS 361 + D S R G + + + + I +GYGLSETSP + E G+ Sbjct: 324 RLDFSGYRCCVGGGMAVQKSVADKWKKLTGCPIIEGYGLSETSPIASANPCTI-DEYTGT 382 Query: 362 VGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGW 421 +G +P+ + + + +DG + V G+ GE+ ++GP V GY + P+ T ++ DG+ Sbjct: 383 IGLPLPSTE--FAILDDDG---QPVPLGQPGEIAIRGPQVMPGYWQRPDETAKVMTPDGF 437 Query: 422 FQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETH 481 F+TGD+G D +G I DR K++I GF V P E+EG + + + + A +G+ E H Sbjct: 438 FKTGDIGVMDERGYTKIVDRKKDMILVSGFNVYPNEVEGVVAQHPGVLECACVGVPDE-H 496 Query: 482 GSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGK 541 E VVR K+ S AA+++ + + +K+ + + F DE+PK GK Sbjct: 497 TGEAVKLFVVRKDKTLS--------AAQLMDYCKEQFTGYKKPK-YIEFRDELPKTNVGK 547 Query: 542 ILRRILKQK 550 ILRR L+ + Sbjct: 548 ILRRELRDE 556 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: 738 Number of extensions: 37 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: 562 Length of database: 566 Length adjustment: 36 Effective length of query: 526 Effective length of database: 530 Effective search space: 278780 Effective search space used: 278780 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