Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate AZOBR_RS31155 AZOBR_RS31155 AMP-dependent synthetase
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__azobra:AZOBR_RS31155 Length = 567 Score = 194 bits (492), Expect = 1e-53 Identities = 153/500 (30%), Positives = 242/500 (48%), Gaps = 44/500 (8%) Query: 69 KGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVT-QASV 127 KG + LF PN+ + + L AGGT+ NP Y EL Q+ +S + +VT V Sbjct: 80 KGVRVGLFLPNTPYFVICYFAILKAGGTVVNFNPLYAERELHHQITDSGVELMVTLDLKV 139 Query: 128 L--PVAREAAKKVGMPEDRIILIGD-------------QRDPDARV----KHFTSVRNIS 168 L +AR A+ G+ I + D +R AR+ +H + R ++ Sbjct: 140 LYGKMARMLAES-GLKRLVICPMADILPFPKNWLFPIVKRAEVARIPADDRHLSFRRLVA 198 Query: 169 GATRYRKQKITPAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGP 228 + I P +DVA L Y+ GTTGVPKG M++H N+ AN Q + W G Sbjct: 199 NDGAPKPVAIDPTEDVAVLQYTGGTTGVPKGAMLTHANLFANTEQCSL-------WFVGA 251 Query: 229 DGKGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVP 288 +R+L LPF+H++ +T ++ ++ G ++++ +F++++ + + + VP Sbjct: 252 RQGEERMLGVLPFFHVFAMTVVMNFSIRIGAEIVMLPRFELDQVMETIHARKPTLFPAVP 311 Query: 289 PVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTH 348 + + H ++KYDLSS+R SG APL E+ EA + +GYGLSE+SP Sbjct: 312 TIYTAINHHRHLEKYDLSSIRYCLSGGAPLPVEVKEAFERNTGCVLVEGYGLSESSPVAT 371 Query: 349 SQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPKEV-GEGEVGELYLKGPNVFLGYHE 407 + +A GS+G +P + +++ EP+ V GE GE+ ++GP V GY Sbjct: 372 ANPITGLNKA-GSIGLPLPGTLIEIVSL----EEPRRVLPVGEKGEVCIRGPQVMKGYWN 426 Query: 408 NPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDA 467 P T L DG TGDVGY D G +I DR+K++I GF V P +E + + A Sbjct: 427 KPSETALTL-VDGRLHTGDVGYMDEDGYTHIVDRIKDMILCSGFNVYPRNVEEAIYLHPA 485 Query: 468 IDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGG 527 + + V G+ E G V V K T ++E +I +L K+ S + Sbjct: 486 VAECVVAGLPDEYRGQTVKAYIRVDDGK-----TLTREE---LIGFLKDKL-SPIEMPKA 536 Query: 528 VHFVDEIPKNPSGKILRRIL 547 + F E+PK GK+ R+ L Sbjct: 537 IEFRGELPKTMIGKLSRKAL 556 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: 766 Number of extensions: 43 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: 567 Length adjustment: 36 Effective length of query: 526 Effective length of database: 531 Effective search space: 279306 Effective search space used: 279306 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