Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_028489631.1 Q394_RS0112845 AMP-binding protein
Query= BRENDA::O74725 (578 letters) >NCBI__GCF_000621325.1:WP_028489631.1 Length = 555 Score = 171 bits (433), Expect = 7e-47 Identities = 155/529 (29%), Positives = 244/529 (46%), Gaps = 47/529 (8%) Query: 58 NRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTIDSLPLFWAVHRLGGVLTPANASYS 117 N VD L R + G + + +A+ N + + R G V+ N Y+ Sbjct: 52 NDVDELTRQFAAYL--IHGAGLKPGERIALMMPNLLQYPIALFGALRAGLVVVNTNPLYT 109 Query: 118 AAELTHQLLDSKAKALVTC-------------VPLLSI-SLEAAAKAGLPKNRIYLLDVP 163 EL HQL DS A A+V VP+ +I + E G PK+ + L V Sbjct: 110 DRELEHQLKDSGATAIVITANFAHTLQDVLDKVPIKTIITTEIGDLFGFPKSLLVNLVVK 169 Query: 164 --EQLLGGVKPPAGYKSVSELTQAGKSLPPVDELRWSAGEGARRTAFVCYSSGTSGLPKG 221 ++++ K P K LT + + A G AF+ Y+ GT+G+ KG Sbjct: 170 YVKKMVPAFKLPTAIKFNQALTLGKQYATRFQD----AEPGHEDIAFLQYTGGTTGIAKG 225 Query: 222 VMISHRNVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQSHIYALVVIGHAGAYRGD 281 ++HRN+IAN LQ +A+ A E+ + LP H++AL G Sbjct: 226 AALTHRNIIANMLQAEAWTT------ADLVAGKEIVITALPLYHVFALTANAMFALKMGA 279 Query: 282 QTIVLPK-FELKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYDLSSVTSLFTGAAP 340 + +++ +L +++ + + + V + +L D+ K D S + + G Sbjct: 280 KNVLITNPRDLPAFIKDLAHEPFTFITGVNTLYNALLNHPDI-GKVDFSRL-KISLGGGM 337 Query: 341 LGMETAADFLKLYPNILIRQGYGLTETCTVVSSTHPHDI--WLGSSGALLPGVEARIVTP 398 ++ A+ K + + + YGLTET V+ +P D+ + G G +P E I Sbjct: 338 AVQKSVAERWKALTGVTLLEAYGLTETSPAVA-INPVDLHDYNGMIGLPVPSTEVSIRDV 396 Query: 399 ENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFV-DGWMRTGDEAVIRRSPKGIEHV 457 + E+ + GEL VR P V+ GY TA V DGW+RTGD AVI + + Sbjct: 397 DGNELDI-GAAGELWVRGPQVMQGYWQRPDETANVMVEDGWLRTGDVAVINE----LGFI 451 Query: 458 FIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVPKAIVVKSASAG 517 +VDR+K+++ V G V P E+E + +HP V + VI PD+ +GE+ KA VVK Sbjct: 452 KLVDRLKDMVLVSGFNVYPNEVEDVLASHPKVLEAGVIGAPDEHSGEIVKAFVVK----- 506 Query: 518 SDESVS-QALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIRD 565 DES++ + L Y + +K K I FV ++PKS GKILR+ +RD Sbjct: 507 KDESLTLEELRAYCRYELSAYKCPK-QIVFVTSLPKSNVGKILRKELRD 554 Lambda K H 0.316 0.134 0.392 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: 32 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: 578 Length of database: 555 Length adjustment: 36 Effective length of query: 542 Effective length of database: 519 Effective search space: 281298 Effective search space used: 281298 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 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. 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