Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate N515DRAFT_1417 N515DRAFT_1417 long-chain acyl-CoA synthetase
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__Dyella79:N515DRAFT_1417 Length = 562 Score = 196 bits (497), Expect = 3e-54 Identities = 158/536 (29%), Positives = 246/536 (45%), Gaps = 44/536 (8%) Query: 43 RHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANP 102 + +Y + + S F L + + KGD +A+ PN + P+ ++G L AG + NP Sbjct: 49 KELSYGQIDELSRQFAGYLTGVLKLGKGDRIAIMMPNVLQYPIALFGALRAGLVVVNTNP 108 Query: 103 GYTVDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGD------------ 150 YT EL QL+++ AK +V + ++ + + IGD Sbjct: 109 MYTARELKHQLEDAGAKAIVVLDNFAATLQQVVAETEVEHIVTTGIGDLLGLKGTLINFV 168 Query: 151 -----QRDPDARVKHFTSVRNI--SGATRYRKQKITPAKDVAFLVYSSGTTGVPKGVMIS 203 + PD R+ H R+ GA + D+AFL Y+ GTTGV KG M+S Sbjct: 169 LKHIKKMVPDYRLPHAVRFRDALAQGAAHPVPKVDLGHDDLAFLQYTGGTTGVAKGAMLS 228 Query: 204 HRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTC--LITQALYKGYHL 261 H N+VAN+ Q G + N P + ++ LP YHI+ LT L+ L G + Sbjct: 229 HGNMVANMLQA----GAWIGTNAKPGE--EVIITALPLYHIFSLTANGLVFTRL-GGLNW 281 Query: 262 IVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQE 321 ++ + D+ + ++ R + V + L P + D S L + G + + Sbjct: 282 LITNPRDMPGFVKELKKSRFTALTGVNTLFNGLLNTPGFAEVDFSRLHLSLGGGMAVQRA 341 Query: 322 LVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGS 381 + E V + + YGL+ETSP D ++ S+G +P+ + + S Sbjct: 342 VAERWKKVTGVTLAEAYGLTETSPAACINPL-DLKDYNSSIGLPIPSTDVAIWS---EDS 397 Query: 382 EPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDR 441 +P +GE VGEL +KGP V GY + P+ T L DGW TGD+ DA G YI DR Sbjct: 398 QPLPIGE--VGELMVKGPQVMQGYWKRPDETAKVLGADGWLHTGDIARMDANGYVYIVDR 455 Query: 442 VKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGT 501 K++I GF V P E+E ++ + + +VA +G+ E H EV VVR K + Sbjct: 456 KKDMILVSGFNVYPNEVEDIVMTHPGVAEVAAVGVPDE-HSGEVVKLFVVR--KDPNLTV 512 Query: 502 SEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQKFKGAAEA 557 E R + +KR + + F D +PK+ GKILRR L+ + K A+ A Sbjct: 513 EALKEFCR------ENLTGYKRPK-LIEFRDALPKSNVGKILRRELRDEKKAASPA 561 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: 700 Number of extensions: 33 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: 562 Length adjustment: 36 Effective length of query: 526 Effective length of database: 526 Effective search space: 276676 Effective search space used: 276676 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