Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_067076571.1 MCUHO_RS08130 acyl--CoA ligase
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_001602375.1:WP_067076571.1 Length = 526 Score = 181 bits (458), Expect = 8e-50 Identities = 161/530 (30%), Positives = 255/530 (48%), Gaps = 60/530 (11%) Query: 41 TQRHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTIS-P 99 T YT L D G+GL L R GD + ++ +S + +V + LW G ++ P Sbjct: 25 TGESYTRAELLDRVCRVGRGLLDLGVGR-GDRVCIYLDSSTEY-LVSYFALWRIGAVAVP 82 Query: 100 ANPGYTVDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDARVK 159 N Y E+ + ++++ A ++T A + L+G RD + ++ Sbjct: 83 TNRVYRESEVLYAVRDAGAVAVITDA-----------------EGAALVGRIRDQASTLR 125 Query: 160 HFTSVRN-ISGATRYRKQKITPAK---------DVAFLVYSSGTTGVPKGVMISHRNIVA 209 H +V +GA + P D+ + Y+SGTTG PKG M++H N +A Sbjct: 126 HVVAVGGEAAGAMPWADLLRAPPDCRAVHCRFDDLCQIQYTSGTTGKPKGAMLTHGNWIA 185 Query: 210 NIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDI 269 + AE ++L D L P H+ GL+ I L G +VM +F++ Sbjct: 186 AMD----AERDVLRITDA-----DVYLGIYPMGHV-GLSWGIA-TLRAGGTYVVMERFEL 234 Query: 270 EKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSR 329 +++ ++YR + +PPV+ L + P + L++ R M SG PLT + + + R Sbjct: 235 DRYLDLARDYRATIVAGMPPVIHSLIQTPPGTETALATARAMISGGGPLTPGVWKPFHER 294 Query: 330 IKVGIKQGYGLSETSP--TTHSQRWEDWREA--MGSVGRLMPNMQAKYMTMPEDGSEP-K 384 + I YGLSET T + R E + A SVG + + K + D ++P + Sbjct: 295 FGIPIVNAYGLSETVVVGTGTAIRPEHYATADEFRSVGTPVGFSEVKIV----DANDPAQ 350 Query: 385 EVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKE 444 E+ G GE+ L+GP V LGY + PE T DGWF TGD+G+ D G YITDR K+ Sbjct: 351 ELRPGVDGEIALRGPGVALGYWQMPEETAAVFLPDGWFLTGDIGHLDEDGMLYITDRKKD 410 Query: 445 LIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEK 504 +I G++V P E+E LV + + D AV G E H EVP+A VV +G S Sbjct: 411 MIVMSGWKVYPTEVEDVLVQHPGVRDAAVFGCTDE-HRGEVPVAVVV----PVGNGISPD 465 Query: 505 DEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQKFKGA 554 + I+ + ++A +K R V +EIP+ K+LR+ L++++ GA Sbjct: 466 E----IVAFARERLAGYKVPR-RVIIAEEIPRVNGWKLLRKRLREEYCGA 510 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: 732 Number of extensions: 38 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: 526 Length adjustment: 35 Effective length of query: 527 Effective length of database: 491 Effective search space: 258757 Effective search space used: 258757 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