Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 3606823 Dshi_0253 AMP-dependent synthetase and ligase (RefSeq)
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__Dino:3606823 Length = 519 Score = 318 bits (816), Expect = 3e-91 Identities = 193/481 (40%), Positives = 275/481 (57%), Gaps = 38/481 (7%) Query: 70 GDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQASVLP 129 GDV+A+ PN D G +AG T++ NP YT +E A QL++S A+ LVT + Sbjct: 68 GDVVAIMAPNMPDYATAFHGAAFAGATVTTLNPTYTTEEAAHQLRDSGAQMLVTVPAFAD 127 Query: 130 VAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAKDVAFLVY 189 +A EA + G+ E +++G S+ + G + + A+D+ L Y Sbjct: 128 LAAEAVQGTGVTET--VMMGTTGPG--------SLEALFGPPLAAQVAVDLARDIVVLPY 177 Query: 190 SSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTC 249 SSGTTG+PKGVM+SHRN+V N+ Q G + D + FLPF+HIYG+T Sbjct: 178 SSGTTGLPKGVMLSHRNLVVNVDQTAEIIGITVQ---------DVTVGFLPFFHIYGMTV 228 Query: 250 LITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLR 309 L+ L +G ++ M +FD+E++ + Q +R YI PPV L L KHP+VD YDLS + Sbjct: 229 LMNCYLSRGAAVVTMPRFDLEQFLSLCQTHRPRQLYIAPPVALALAKHPMVDDYDLSGVE 288 Query: 310 MMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNM 369 + SGAAPL ++ EAV R+ V + QGYG++E SP +H + GSVG P+ Sbjct: 289 FILSGAAPLGGDVAEAVGRRLGVEMVQGYGMTEMSPVSHFT--PPGQNVPGSVGPTAPSA 346 Query: 370 QAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGY 429 +++ + PE G + E GE++++GP + GY P+AT ++ DGW +TGD+G Sbjct: 347 ESRIVD-PETGEDAAE------GEVWVRGPQIMQGYLNRPDATAETVTRDGWLKTGDLGR 399 Query: 430 QDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMAC 489 D GN +ITDRVKELIK GFQV PAELE L+ + AI D AVIG+ ++ G E PMA Sbjct: 400 FDEAGNLFITDRVKELIKVSGFQVAPAELEAVLLTHPAITDAAVIGVPDDSAG-ERPMAF 458 Query: 490 VVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQ 549 VVRS S G +I +A +KR+ V FV+ +PK+ SGKILRR+L+ Sbjct: 459 VVRSDPDLSEGA--------VIAHAAEHLAHYKRI-ARVAFVEAVPKSASGKILRRLLRA 509 Query: 550 K 550 K Sbjct: 510 K 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: 709 Number of extensions: 27 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: 519 Length adjustment: 35 Effective length of query: 527 Effective length of database: 484 Effective search space: 255068 Effective search space used: 255068 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