Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_036258835.1 DL86_RS04845 malonyl-CoA synthase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000746085.1:WP_036258835.1 Length = 507 Score = 180 bits (457), Expect = 1e-49 Identities = 159/536 (29%), Positives = 250/536 (46%), Gaps = 37/536 (6%) Query: 20 FLFER-KDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTP 78 +LF+ +DR P D I+ ++Y AS L AL + GD +A Sbjct: 4 YLFQMIRDRIGPPDDRIFLQTPGGPDFSYGDAVAASARSAAALSALGV-KPGDRVAAQVE 62 Query: 79 NSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLPVAREAAKKV 138 S ++ G + AG P NP YT+ E+A+ L ++ ++ K Sbjct: 63 KSAAAVMLYLGAVRAGAIFLPLNPAYTLAEIAYFLSDAEPAVVICDPDRRGELASLVAKA 122 Query: 139 GMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDVAFLVYSSGTTGVPK 198 G P L D R A + T + S A R D+A ++Y+SGTTG K Sbjct: 123 GAPLLET-LGADGRGSFADLCA-TQSGDFSDAAR-------GPDDLAAILYTSGTTGRSK 173 Query: 199 GVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKG 258 G M++H N+ +N A + +W P D +L LP YH +GL I L+ Sbjct: 174 GAMLTHANLASN------AATLVEAWRFTP---ADVLLHALPIYHTHGLFVAINTILFSA 224 Query: 259 YHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPL 318 ++ +++FD ++ A + + S VP L + P V + + +R+ SG+APL Sbjct: 225 GRILFLARFDADECLALMP--QASAMMGVPTFYTRLLRRPDVLRRASAHMRLFISGSAPL 282 Query: 319 TQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPE 378 E R I + YG++ET+ + D G+VG +P + + + PE Sbjct: 283 LAETHREWVERTGHAILERYGMTETNMIASNPY--DGERIAGTVGPPLPGVAVR-IADPE 339 Query: 379 DGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYI 438 G++ +G ++G + +KGPNVF GY NPE T DG+F TGD+G DA G +I Sbjct: 340 TGAD---LGRDKIGVIEVKGPNVFKGYWRNPEKTAAEFRADGFFITGDLGKIDANGYVHI 396 Query: 439 TDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKS 498 R K+LI GF V P E+E + + + AV+G+ E G + A VVR + Sbjct: 397 IGRAKDLIITGGFNVYPKEVEAEIDAIAGVVESAVVGLPHEDFGEGI-AAIVVR---TPG 452 Query: 499 SGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQKFKGA 554 SG E A + L++++A K L V FV+E+P+N GK+ + L++ +KG+ Sbjct: 453 SGLDE----AGVRSALENRLAKFK-LPKRVIFVEELPRNAMGKVQKNALRETYKGS 503 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: 657 Number of extensions: 31 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: 507 Length adjustment: 35 Effective length of query: 527 Effective length of database: 472 Effective search space: 248744 Effective search space used: 248744 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: 52 (24.6 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