Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_011951133.1 SWIT_RS01410 AMP-dependent synthetase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000016765.1:WP_011951133.1 Length = 492 Score = 134 bits (338), Expect = 6e-36 Identities = 113/372 (30%), Positives = 185/372 (49%), Gaps = 30/372 (8%) Query: 187 LVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYG 246 +VY+SGTTG PK V R + A+ + A+ + G+ L P YH++G Sbjct: 142 MVYTSGTTGRPKAV----RRLPASGEES--AQRARVLAAIHDSAPGNVALVTGPLYHLFG 195 Query: 247 LTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHP--VVDKYD 304 L+T G +++M +FD E A ++ +R + S +VP + + L + P V +YD Sbjct: 196 -QALMTATFGAGGSVVIMERFDPEACLALIERHRVTHSALVPTLFVRLLRLPDAVKARYD 254 Query: 305 LSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGR 364 LSSLR + AP E+ A+ + + YG +ET T E W E GSVGR Sbjct: 255 LSSLRHVVHSGAPCAPEVKRAMLGWWGPVLHETYGSTETGVVTKIGPAE-WLERPGSVGR 313 Query: 365 LMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLK--GPNVFLGYHENPEATKGCLSEDGWF 422 P + + EDG G VG++YL+ G F +H +P A + + DG Sbjct: 314 --PVLTGEVRIRGEDGGWAPA---GTVGDVYLRIHGTPDFT-FHGDP-AKRAAVEHDGLV 366 Query: 423 QTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHG 482 GD+G+ DA+G ++ DR +++ G + PAE+E L+++ AI D AV G+ +G Sbjct: 367 TCGDIGWLDAQGYLFLCDRRVDMLISGGVNIYPAEIEAALLEHRAIGDCAVFGVPDPEYG 426 Query: 483 SEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKI 542 E P+A V ++ +A + +L ++A +K R + D +P+ +GKI Sbjct: 427 -EAPVAYVQPASAI---------DAGAVRAFLRGRLAGYKVPR-HIVLTDALPREETGKI 475 Query: 543 LRRILKQKFKGA 554 ++R L+++F A Sbjct: 476 MKRKLREQFLAA 487 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: 660 Number of extensions: 40 Number of successful extensions: 5 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: 492 Length adjustment: 35 Effective length of query: 527 Effective length of database: 457 Effective search space: 240839 Effective search space used: 240839 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 Sep 24 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