Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF4155 Psest_4228 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= BRENDA::O74725 (578 letters) >FitnessBrowser__psRCH2:GFF4155 Length = 541 Score = 179 bits (455), Expect = 2e-49 Identities = 157/536 (29%), Positives = 248/536 (46%), Gaps = 35/536 (6%) Query: 39 RDPYTCGITGKSYSSKEVANRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTIDSLPL 98 R ++CG +Y+ E+ +R D+ AR L G P + LA+ N + Sbjct: 35 RTAFSCGDDHLTYA--ELGSRADAFARYLRYHAGLQPGD------RLALQLPNCLQYPIA 86 Query: 99 FWAVHRLGGVLTPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLPKNRIY 158 + + G V+ N Y+AAE HQ DS AKA++ LL A L + + Sbjct: 87 VFGALKAGLVIVNTNPQYTAAEARHQFHDSGAKAILVLDRLLPQVRAVQADTALRQIILT 146 Query: 159 LLDVPEQLLGGVKPPAGYKSVSELTQAGKSLPPVDELRWSAGEGARRTAFVCYSSGTSGL 218 +D +Q + + + + L + G+ PV G R A + Y+ GT+G+ Sbjct: 147 SVDDLQQPIYESQEDGTLRFMQAL-RLGEQRSPVQR-----EAGLDRLALLQYTGGTTGV 200 Query: 219 PKGVMISHRNVIANTLQ-IKAFEQNYRDGGGTKPASTEVALGLLPQSHIYALVVIGHAGA 277 KG M++HRN++AN LQ I+ F+Q G +V + LP HI A + Sbjct: 201 SKGAMLTHRNLLANVLQTIELFDQP-----GLLEPEKDVRIAPLPLYHIMAFATNCLSSV 255 Query: 278 YRGDQTIVLPKFE-LKSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKYDLSSVTSLFT 336 G T+ + L + A+Q++ S L + + + ++ + S D S + + Sbjct: 256 GMGLHTVFIRDGRNLDETIGAMQRHPFSLLSGINTLFVGLMNHPEFRS-IDFSHLKWATS 314 Query: 337 GAAPLGMETAADFLKLYPNILIRQGYGLTETCTVVSS-THPHDIWLGSSGALLPGVEARI 395 G APL E + L IR+G+GLTE VV++ T G G L E R Sbjct: 315 GGAPLNSEVGRRWQAL-TGAPIREGFGLTEASPVVATGTQLSPYREGYIGQALIETELRT 373 Query: 396 VTPENKEITTYDSPGELVVRSPSVVLGYLNNEKATAETFV-DGWMRTGDEAVIRRSPKGI 454 V E ++ ++PGEL +R P V+ GY TA+ DGW++TGD A++ Sbjct: 374 VDDEGNDVPP-ETPGELWLRGPQVMQGYWQRPDETAKVLTPDGWLKTGDIALLDVDG--- 429 Query: 455 EHVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVPKAIVVKSA 514 V IVDR K++I V G V P E+E ++ HP V +C + +PD R GE K V Sbjct: 430 -FVKIVDRKKDMILVSGFNVFPNEIEDVLMQHPSVRECVAVGVPDARKGEAVKVFV---- 484 Query: 515 SAGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIRDQEKEA 570 S D +AL+++ + +K + + D +PK+ GK+LRR +RD+ + A Sbjct: 485 SLKDDTVDERALLEHCRQYLTGYK-MPSFLELRDELPKTAVGKLLRRQLRDEARAA 539 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: 674 Number of extensions: 26 Number of successful extensions: 7 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: 541 Length adjustment: 36 Effective length of query: 542 Effective length of database: 505 Effective search space: 273710 Effective search space used: 273710 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 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