Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF1907 HP15_1864 acyl-CoA synthase
Query= BRENDA::D3GE78 (556 letters) >FitnessBrowser__Marino:GFF1907 Length = 560 Score = 188 bits (477), Expect = 5e-52 Identities = 157/523 (30%), Positives = 247/523 (47%), Gaps = 34/523 (6%) Query: 46 LTTHDLRLWSQRLAAGLR-KSGLQRGDRVLLFSGNDLFFPVVFLGVIMAGGIFTGANPTF 104 LT DL S+ AA L+ K+ L+ GDR+ + N +PVV G + AG I NP + Sbjct: 53 LTYRDLDTQSRNFAAWLQNKTDLKPGDRIAVQMPNVSQYPVVVFGAMRAGLIVVNTNPLY 112 Query: 105 VARELAYQLQDSGATYLLCASNSLE--------TGLEAAKQAKLPQSHIFAYDTSIYDGV 156 RE+ +Q DSGA L+ +N E TG+E ++ H T + V Sbjct: 113 TTREMEHQFNDSGAKALVVLANMAENAEKVLPHTGIEHVIVTEIADMHSPIKRTLMNAVV 172 Query: 157 TNPQKGCAYWS-----DLLASEEEGAAFTWDELSTPA--LSSTTLALNYSSGTTGRPKGV 209 + +K ++ L A GA E TP L Y+ GTTG KG Sbjct: 173 KHVKKMVPPFNLPQAHKLPAVLSAGAR----EKFTPVECKQDDIAVLQYTGGTTGVAKGA 228 Query: 210 EISHRNYVANMLQYCHTASLHPDYKARLERSRWLCFLPMYHAMAQNIFIAAALYR-ATPV 268 ++H N VAN+LQ T + D + + LP+YH + + L A V Sbjct: 229 MLTHGNLVANLLQ---TRPMMEDMVVEGQEVV-IAPLPLYHIYSFTLNCGIMLEAGAHNV 284 Query: 269 YIMSKFDFVKMLEYTQRFRITDFILVPPVVVALAKHPAVGQYDLSSVELVGSGAAPLGRE 328 I + D ++ + + T F+ + + VAL + D SS++L SG G Sbjct: 285 LIPNPRDIPGFVKELKNHKFTAFLGLNTLFVALCNNEDFQDLDFSSLKLTSSG----GMA 340 Query: 329 VCEEVEKLWPPGK-INIKQGWGMTEATCSVTGWNPAEISTSASVGELNANCEAKIMFDGV 387 + + K+W I +G+GMTE + VT +NP ++G + K + + Sbjct: 341 LTSDTAKMWERVTGCEICEGFGMTETSPVVT-FNPHSAIQIGTIGLPIPSTVVKTLDEEG 399 Query: 388 EVKERNSRGELWVRAPNVMKGYWRNEKATKETKTEDGWLLTGDIAFVDDDGKFHVVDRMK 447 GEL V+ P VM+GYW+ + T+++ TEDG+L TGDIA + +DG +VDR K Sbjct: 400 NETPLGEPGELCVKGPQVMRGYWQRPEDTQKSFTEDGYLRTGDIALIQEDGYIRIVDRKK 459 Query: 448 ELIKVKGNQVAPAELEALLLEHPAISDVAVIGVV-INNDERPRAYVVLRPGQSATANEIA 506 ++I V G V P E+E ++ HP + + A +GV + E + Y+V + T NE+ Sbjct: 460 DMIIVSGFNVFPNEIEDVVSSHPKVVECAAVGVPDAKSGEAVKVYLV-PTAEGVTENELK 518 Query: 507 HYLDNKVSAFKRITGGVVFLEAIPKNPSGKILRMKLREQAKEE 549 + +++A+K + F + +PK GKILR +LR++A + Sbjct: 519 EFCRERLTAYK-VPKKFEFRDELPKTNVGKILRRELRDEANNK 560 Lambda K H 0.319 0.134 0.403 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: 647 Number of extensions: 36 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 556 Length of database: 560 Length adjustment: 36 Effective length of query: 520 Effective length of database: 524 Effective search space: 272480 Effective search space used: 272480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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