Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_013645675.1 METBO_RS10410 AMP-binding protein
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000191585.1:WP_013645675.1 Length = 552 Score = 182 bits (462), Expect = 3e-50 Identities = 159/556 (28%), Positives = 261/556 (46%), Gaps = 59/556 (10%) Query: 22 FERKDRAYPD-DKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNS 80 FE++ P D ++Y D D + +TYK + KGL ++ +KGD + ++ N Sbjct: 12 FEKQVEKDPSRDFLVYPDRDLR--FTYKQFDERVNMLAKGLLSIGV-KKGDHVGIWAKNV 68 Query: 81 IDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVT-----QASVLPVAREAA 135 D M+ T G + N Y EL + LK S K L L + + Sbjct: 69 PDWLTFMFATAKIGVVLVTMNTAYKSHELEYVLKQSDMKALAIIDGFRDVDYLKILYDLV 128 Query: 136 KKVGMPE------------DRIILIGDQRDPDARVKHFTSVRNISGA----TRY-RKQKI 178 ++ E ++I +G ++ R + T+ + G T + R +K Sbjct: 129 PELRTHERGELKSERFPYLKQVIYVGQEKH---RGMYNTNELMLLGKHTDDTEFLRVKKT 185 Query: 179 TPAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAF 238 DV + Y+SGTTG PKGVM++HRNI+ N +I E + + + D++ Sbjct: 186 LDNHDVINMQYTSGTTGFPKGVMLTHRNILNN--GYYIGECQKFT-------EEDKLCLP 236 Query: 239 LPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHP 298 +P +H +G+ + L L+++ +FD A VQ C+ Y VP + + HP Sbjct: 237 VPLFHCFGIVLGVLAILTHRGTLVMLEEFDPLLALAAVQKESCTALYGVPTMFIAEFNHP 296 Query: 299 VVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKV-GIKQGYGLSETSPT-THSQRWEDWR 356 + + +DL+SLR +P E ++ V S + + I YGL+E SP T + + Sbjct: 297 MFEMFDLTSLRTGIMAGSPCPIEAMKKVISDMHMEDITIAYGLTEASPVFTQTSVDDSVE 356 Query: 357 EAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCL 416 + + +VGR PN++ K + PE G + +G G+ GE+ +G NV GY++ P+ TK + Sbjct: 357 KRVNTVGRARPNIEVKLID-PETG---ETLGPGQPGEICCRGYNVMKGYYKMPDKTKEAI 412 Query: 417 SEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGI 476 EDGW +GD+ D G + I R+K++I G + P E+E ++ + DV V+GI Sbjct: 413 EEDGWLHSGDLATVDKDGYYTIVGRIKDMIIRGGENIYPREIEEFIHTMPEVQDVQVVGI 472 Query: 477 ESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPK 536 E +G E+ A V+ K E+D + + K+A +K + V V+E P Sbjct: 473 PDEKYG-EIVGAFVI---PEKDVDLEEED----VRDYALQKIARYK-VPKHVFIVEEFPL 523 Query: 537 NPSGKILRRILKQKFK 552 SGKI QKFK Sbjct: 524 TTSGKI------QKFK 533 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: 667 Number of extensions: 32 Number of successful extensions: 3 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: 552 Length adjustment: 36 Effective length of query: 526 Effective length of database: 516 Effective search space: 271416 Effective search space used: 271416 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 Apr 09 2024. 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