Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate BPHYT_RS15945 BPHYT_RS15945 AMP-binding protein
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__BFirm:BPHYT_RS15945 Length = 520 Score = 168 bits (426), Expect = 4e-46 Identities = 149/491 (30%), Positives = 231/491 (47%), Gaps = 41/491 (8%) Query: 64 LYEW--RKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGL 121 L EW R GD + + NSI V+++ T +N + EL +HA Sbjct: 64 LREWGVRGGDRVMIVAENSIVQIVLLFATARLDAWALVSNARLSAAEL--DSIRAHA--- 118 Query: 122 VTQASVLPVAREAAKKVGMPEDRIILI-GDQRDPDARVKHFTSVRNISGATRYRKQKITP 180 Q ++ A E++ + +R PD +T + A + Sbjct: 119 --QPRIVAYATESSADAKLHAERHHAAKAPAFTPDIGAWSYT----VDSAAVAEPVEAAS 172 Query: 181 AKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLP 240 + A L+Y++GTTG PKGVM+SHRN++ FIA GPD D V A LP Sbjct: 173 ERQCAALIYTTGTTGAPKGVMLSHRNLL------FIAAISSRLRKVGPD---DVVYAVLP 223 Query: 241 FYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVV 300 H+YG + +L+ G L ++ +F E + + R S VP + L +H Sbjct: 224 ISHVYGFASVCLGSLHAGATLRLVPRFAPEAVRRALADERVSIFQGVPAMHAKLLEHLQT 283 Query: 301 DKYDLSS--LRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREA 358 + S+ LR SG +PL L V S + + GYG++E+SPT S D + Sbjct: 284 HGHAWSAPHLRFAYSGGSPLDAALKAQVESVCGLPLHNGYGMTESSPTV-SHTMLDAPRS 342 Query: 359 MGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSE 418 SVG ++P ++ +++ G + + +G++GEL+++GPNV LGY+ + E T+ ++E Sbjct: 343 DCSVGEVIPGVEVRFV-----GLDGIDAAQGDIGELWVRGPNVMLGYYRSLEQTRAAVTE 397 Query: 419 DGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIES 478 DGW +TGD+ QDA G +I R KELI GF V PAE+E L + + AVIG Sbjct: 398 DGWLKTGDLARQDADGALHIVGRSKELIIRSGFNVYPAEVEHVLNAHPQVVQSAVIGRAV 457 Query: 479 ETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNP 538 E G+E +A V T A +I ++A +KR V + +P Sbjct: 458 E--GNEEVVAFV-------ELLTGATVTPAELIDCCGERLAPYKR-PAEVKVLAALPAAS 507 Query: 539 SGKILRRILKQ 549 +GKIL+ L++ Sbjct: 508 TGKILKHRLRE 518 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: 586 Number of extensions: 31 Number of successful extensions: 4 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: 520 Length adjustment: 35 Effective length of query: 527 Effective length of database: 485 Effective search space: 255595 Effective search space used: 255595 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: 52 (24.6 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