Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate Dsui_3212 Dsui_3212 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__PS:Dsui_3212 Length = 555 Score = 185 bits (469), Expect = 5e-51 Identities = 164/568 (28%), Positives = 258/568 (45%), Gaps = 59/568 (10%) Query: 10 VDIPEVDLWTFLFERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRK 69 VD+ E LFE+ Y D ++ Y + TY L S DF L+ + + + Sbjct: 17 VDVNEFKSLGQLFEQSCAQYRD-RVAYINMGVG--ITYGELDRLSRDFAAYLQDVLKLPQ 73 Query: 70 GDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLP 129 G +AL PN + PV M+G L AG + NP YT EL QLK+S A+ +V + Sbjct: 74 GARVALMMPNLLQYPVCMFGALRAGYVVVNCNPLYTHRELEHQLKDSGAEAIVIVENFAH 133 Query: 130 VAREAAKKV-GMPEDRIILIGDQRDP------DARVKHFTSVRNISGATRYRKQKITPAK 182 +A V G+ + +GD + V+H + R+ K K A+ Sbjct: 134 TLEQALPLVPGLKHVIVTSLGDMLGALKGTVVNLVVRHVKKMVPAWKLPRHVKFKAAMAR 193 Query: 183 --------------DVAFLVYSSGTTGVPKGVMISHRNIVANIRQQ------FIAEGEML 222 D+A+L Y+ GTTGV KG M+ HRNI+AN++Q F+ + + L Sbjct: 194 GKGATLRPVQVGHEDIAYLQYTGGTTGVAKGAMLLHRNIIANLQQAHAWIEPFLHKDQQL 253 Query: 223 SWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKGY-HLIVMSKFDIEKWCAHVQNYRC 281 ++ LP YHI+ LT L G ++++ + DI + + Y+ Sbjct: 254 ------------IITALPLYHIFSLTANCLTFLKIGATNVLITNPRDIPGFVKELAQYKF 301 Query: 282 SFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLS 341 + V + L +P K D S+LR G + + + + + + YGL+ Sbjct: 302 TVITGVNTLFNALLNNPDFAKLDFSALRAALGGGMAVQKSVAQKWRQVTGKPLIEAYGLT 361 Query: 342 ETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNV 401 ETSP D E G++G +P + + + G++ + G+ GE+ ++GP V Sbjct: 362 ETSPAATINPL-DLGEFNGAIG--LPISSTEIVIRDDLGND---LPVGQAGEICIRGPQV 415 Query: 402 FLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGY 461 GY P+ T DG+ +TGDVG D KG I DR K++I GF V P E+E Sbjct: 416 MKGYWLRPDETATVFYADGFLRTGDVGVMDEKGFVRIVDRKKDMILVSGFNVYPNEVEAV 475 Query: 462 LVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASH 521 + + A+ +VA +G+ SE G V + V++ S T E ++I + + Sbjct: 476 VAMHPAVMEVAAVGVPSEHSGEAVKIFVVLKD----KSVTKE-----QLIAHCKENLTGY 526 Query: 522 KRLRGGVHFVDEIPKNPSGKILRRILKQ 549 K + V F D++PK GKILRR LK+ Sbjct: 527 K-VPHLVEFRDDLPKTNVGKILRRALKE 553 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: 662 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: 555 Length adjustment: 36 Effective length of query: 526 Effective length of database: 519 Effective search space: 272994 Effective search space used: 272994 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 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