Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_041099422.1 SUTH_RS11630 AMP-binding protein
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000828635.1:WP_041099422.1 Length = 528 Score = 178 bits (451), Expect = 5e-49 Identities = 149/494 (30%), Positives = 238/494 (48%), Gaps = 46/494 (9%) Query: 68 RKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASV 127 R GD L L NSI V+ + P N + E+ + +S A+ +V ++V Sbjct: 69 RAGDRLLLVAENSIPVVVLALACSRLDAWLVPINARLSQREIDTFVDHSGARLVVFTSAV 128 Query: 128 LPVAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDVAFL 187 P A A+++G E P H TS NI+ A + I + VA L Sbjct: 129 SPEAEAHAQRLGAAEVDW--------PGCGRFHLTSA-NIAVAP---EPTIADGEQVAAL 176 Query: 188 VYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGL 247 +Y+SGT+G PK VM++HRN++ FIAE P DRV A LP HIYGL Sbjct: 177 IYTSGTSGAPKAVMLTHRNLL------FIAENGRCMRRQTP---ADRVYAVLPLSHIYGL 227 Query: 248 TCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLL---GKHPVVDKYD 304 + AL+ G L++ +F+ A ++ R + + VP + L G+ P ++ Sbjct: 228 ATMALSALHAGASLVLAPRFEPAAVAAALETGRVTILHGVPAMYAKLLEWGRRPG-NRLC 286 Query: 305 LSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGR 364 +LR+ G APL Q + + + + + GYG++E SP+ R + R SVG Sbjct: 287 APALRIAQGGGAPLDQSFKDDFEAAVGITLHNGYGMTEASPSIAQTRLDAPRRDC-SVGP 345 Query: 365 LMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQT 424 +P + + + +DG++ V GEVGEL+++GP V GY++ PE T+ + +GW T Sbjct: 346 PIPGIGIRIV---KDGAD---VAPGEVGELHVRGPGVMKGYYKAPELTREAVDAEGWLNT 399 Query: 425 GDVGYQDAK----GNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESET 480 GD+ Q+ + G +I R KELI GF V P E+E + + + AV+G + Sbjct: 400 GDLARQEQEEGGDGALFIVGRSKELIIRSGFNVYPIEVEQAINSHPDVVHCAVVG--RDV 457 Query: 481 HGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSG 540 G+E +A V G S +A + WL +++ +K + + ++ +P +G Sbjct: 458 PGNEEVVAYV-----ELVPGRSLAPQA--LAAWLHERLSPYK-IPSHIELLEHLPATATG 509 Query: 541 KILRRILKQKFKGA 554 KIL+ L+Q GA Sbjct: 510 KILKNQLRQMAAGA 523 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: 642 Number of extensions: 37 Number of successful extensions: 7 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: 528 Length adjustment: 35 Effective length of query: 527 Effective length of database: 493 Effective search space: 259811 Effective search space used: 259811 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