Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_011159254.1 TX73_RS18970 dicarboxylate--CoA ligase PimA
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000195775.1:WP_011159254.1 Length = 552 Score = 199 bits (506), Expect = 2e-55 Identities = 162/524 (30%), Positives = 253/524 (48%), Gaps = 42/524 (8%) Query: 43 RHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANP 102 R TY L + L A R V AL+ N+ D P+ +G L AG + +P Sbjct: 46 RQITYTKLEAMAETAAAALLAAGYGRDSSV-ALYIGNTPDHPINFFGALKAGARVVHLSP 104 Query: 103 GYTVDELAFQLKNSHAKGLVT--QASVLPVAREAAKKVGMPEDRIILIGDQR-------- 152 L+ +L +S A+ L+T A++LP+A K + DR+I+ D Sbjct: 105 LDGERALSHKLSDSGARVLITTDSAALLPMAERFLAKGLL--DRLIVCSDASWGESATPL 162 Query: 153 ---DPDARVKHFTSVRNISGATRYRKQKITPAKDVAFLVYSSGTTGVPKGVMISHRNIVA 209 D RV T I GA++ D+A L Y+ GTTG+PKG M++H N+ + Sbjct: 163 APLPSDPRV--ITYADFIKGASKPMAWPAIVPDDIALLQYTGGTTGLPKGAMLTHSNLTS 220 Query: 210 NIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDI 269 + + G + + +GG RV+ LP +HIY LT ++ + L +G + + +FD+ Sbjct: 221 AVAI-YDVWGLVRANSGGIH----RVICVLPLFHIYALTVILLRCLKQGDLISLHQRFDV 275 Query: 270 EKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSR 329 ++ R + VP + + L P ++K DLSSL M SG APL E+ + Sbjct: 276 AAVFRDIEEKRATVFPGVPTMWIALANDPSLEKRDLSSLTMAGSGGAPLPVEVARLFERK 335 Query: 330 IKVGIKQGYGLSET-SP-TTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEV- 386 + +K G+G++ET SP T H D GS+G ++P ++ + + +PK V Sbjct: 336 TNLKLKSGWGMTETCSPGTGHPPEGPD---KPGSIGLMLPGIELDVVAL----DDPKRVL 388 Query: 387 GEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELI 446 GEVGEL ++GPNV GY PE + D F TGD+GY D G F++ DR K++I Sbjct: 389 PPGEVGELRVRGPNVTKGYWNRPEESAHSFVGDR-FLTGDIGYMDQDGYFFLVDRKKDMI 447 Query: 447 KYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDE 506 GF V P +E + ++ A+ +V VIG+ + G E A V +K E Sbjct: 448 ISGGFNVYPQMIEQAIYEHPAVQEVIVIGVPDDYRG-EAAKAFVKLREGAKPFSIDE--- 503 Query: 507 AARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQK 550 + +L K+ H+ L V F+DE+P+ GK+ R L+ + Sbjct: 504 ---LRAFLTGKLGKHE-LPTAVEFLDELPRTTVGKLSRHELRSQ 543 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: 708 Number of extensions: 34 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: 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 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