Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_043745116.1 AMB_RS18140 malonyl-CoA synthase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000009985.1:WP_043745116.1 Length = 508 Score = 174 bits (440), Expect = 1e-47 Identities = 146/484 (30%), Positives = 229/484 (47%), Gaps = 35/484 (7%) Query: 68 RKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASV 127 + GD +A+ S + V+ L +G + P N Y EL + L ++ +V Q S Sbjct: 52 KPGDRVAVQVDKSAEAVVLYLACLRSGAVLLPLNTAYQAGELEYFLFDAAPSAVVCQPSR 111 Query: 128 LPVAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDVAFL 187 L A G+ ++ +G D T G + D+A + Sbjct: 112 LAELEGLAVAAGIGTC-VMTLGSHGDG-------TLPERAKGLSETFATVPRGGDDMAAI 163 Query: 188 VYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGL 247 +YSSGTTG PKG M+SH N+ +N A+ W PD D +L LP +H +GL Sbjct: 164 LYSSGTTGRPKGAMMSHTNLGSN------AQTLHDLWGFRPD---DVLLHCLPIFHTHGL 214 Query: 248 TCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSS 307 I L G +I KFD E+ ++ R + VP P + S Sbjct: 215 FVAINCVLLNGSPMIFCPKFDAEQAIGLLK--RATVFMGVPTFYTRFLTSPNLTPEACSH 272 Query: 308 LRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMP 367 +R+ SG+APL +E A + I + YG++E T + D R G+VG +P Sbjct: 273 MRLFISGSAPLLEETFNAFKDKTGFTILERYGMTEGGMFTSNPLVGDRRA--GTVGFPLP 330 Query: 368 NMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDV 427 ++Q + G E + + +GEVG + +KGPN+F GY PE TK +EDG+F++GDV Sbjct: 331 DVQLRIT-----GEEGQVLPQGEVGIIEVKGPNIFKGYWNMPEKTKSDFTEDGFFKSGDV 385 Query: 428 GYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPM 487 G DA+G I R K+LI G+ V P E+E ++ + + AV+G+ G E + Sbjct: 386 GVVDARGYVSIVGRAKDLIISGGYNVYPKEVEDFIDRLAGVVESAVVGMPHPDFG-EAGL 444 Query: 488 ACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRIL 547 A VV A+ +S T+E +I L ++A++K + V V E+P+N GK+ + +L Sbjct: 445 AIVV--AEKGASLTAE-----GVIDSLKGRLANYKVPKLAV-VVTELPRNAMGKVQKNVL 496 Query: 548 KQKF 551 + + Sbjct: 497 RDSY 500 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: 674 Number of extensions: 40 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: 508 Length adjustment: 35 Effective length of query: 527 Effective length of database: 473 Effective search space: 249271 Effective search space used: 249271 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 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