Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate H281DRAFT_04125 H281DRAFT_04125 Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__Burk376:H281DRAFT_04125 Length = 520 Score = 174 bits (441), Expect = 8e-48 Identities = 153/492 (31%), Positives = 233/492 (47%), Gaps = 43/492 (8%) Query: 64 LYEW--RKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGL 121 L +W R GD + + NSI V+++ T +N + EL +HA+ Sbjct: 64 LRDWGVRGGDRVMIVAENSIAQIVLLFATARLDAWALVSNARLSASEL--DAIRAHAQPR 121 Query: 122 VTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPA 181 VT V E++ G R G PD V + + T + + + A Sbjct: 122 VTAYVV-----ESSADAGQHAQRH---GASAAPD--VAPGIGAWSFTVDTFAQAEPVEAA 171 Query: 182 KD--VAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFL 239 D A L+Y++GTTG PKGVM+SHRN++ FIA PD D V A L Sbjct: 172 NDRQCAALIYTTGTTGAPKGVMLSHRNLL------FIAAVSSRLRQVRPD---DVVYAVL 222 Query: 240 PFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPV 299 P H+YG + +LY G L + +F + + R S VP + L +H Sbjct: 223 PISHVYGFASVCLGSLYAGATLRLAPRFAPGAVRRALADERVSIFQGVPAMHAKLIEHLQ 282 Query: 300 VD--KYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWRE 357 + LR + SG +PL L V S + + GYG++E+SPT SQ D Sbjct: 283 THGHAWHAPHLRFIYSGGSPLDAALKAHVESVYGLPLHNGYGMTESSPTV-SQTMLDAPR 341 Query: 358 AMGSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLS 417 SVG ++P ++ +++ G + +V GE GEL+++GPNV LGY+ NP+ T+ ++ Sbjct: 342 RDCSVGEVIPGVEVRFV-----GLDGADVAVGETGELWVRGPNVMLGYYRNPQQTRAAVT 396 Query: 418 EDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIE 477 +DGW +TGD+ QDA G +I R K+LI GF V PAE+E L + + AVIG Sbjct: 397 QDGWLKTGDLARQDADGALHIVGRSKDLIIRSGFNVYPAEVEHVLNAHPQVVQSAVIGRP 456 Query: 478 SETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKN 537 E G+E +A V +A + + A + W ++A +KR V + +P Sbjct: 457 VE--GNEEVIAFVELAANASVT-------PAELTAWCVERLAPYKR-PAEVKVLAALPAA 506 Query: 538 PSGKILRRILKQ 549 +GKIL+ L++ Sbjct: 507 STGKILKHRLRE 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: 587 Number of extensions: 26 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