Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate 352309 BT2782 long-chain-fatty-acid--CoA ligase (NCBI ptt file)
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__Btheta:352309 Length = 549 Score = 159 bits (402), Expect = 3e-43 Identities = 141/550 (25%), Positives = 242/550 (44%), Gaps = 57/550 (10%) Query: 23 ERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSID 82 E D+ Y I+Y D + + +T+ L D KGL A+ R G + ++ N D Sbjct: 18 ETPDKEY----IVYSDRNLR--FTWSQLNQRVDDMAKGLIAVGVER-GTHVGIWAANVPD 70 Query: 83 TPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGL-----------VTQASVLPVA 131 +++ G N Y EL + +NS L V + Sbjct: 71 WLTLLYACAKIGAVYVTVNTNYKQAELEYLCQNSDMHTLCIVNGEKDSDFVQMTYTMLPE 130 Query: 132 REAAKKVGMPEDR------IILIGDQRDPDARVKHFTSVRNISGATRYRKQKITPAK--- 182 + ++ + +R +I +G ++ + + + ++T K Sbjct: 131 LKTCERGHLKSERFPYMKNVIYVGQEKHRGM----YNTAEILLLGNNVEDDRLTELKSKV 186 Query: 183 ---DVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFL 239 DV + Y+SGTTG PKGVM++H NI N GE + + D++ + Sbjct: 187 DCHDVVNMQYTSGTTGFPKGVMLTHYNIANN----GFLTGEHMKFTAD-----DKLCCCV 237 Query: 240 PFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPV 299 P +H +G+ L G +++ +FD A + RC+ Y VP + + HP+ Sbjct: 238 PLFHCFGVVLATMNCLTHGCTQVMVERFDPLVVLASIHKERCTALYGVPTMFIAELHHPM 297 Query: 300 VDKYDLSSLRMMNSGAAPLTQELVEAVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAM 359 D +D+S LR + EL++ V ++ + + YGL+E +P + R +D + Sbjct: 298 FDLFDMSCLRTGIMAGSLCPVELMKQVEEKMYMKVTSVYGLTEAAPGMTATRIDDSFDVR 357 Query: 360 -GSVGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGYHENPEATKGCLSE 418 +VGR + + + PE G +E G GE+ +G N GY++NPEAT + + Sbjct: 358 CNTVGRDFEFTEVRVID-PETG---EECPVGVQGEMCNRGYNTMKGYYKNPEATAEVIDK 413 Query: 419 DGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIES 478 D + +GD+G +D GN+ IT R+K++I G + P E+E +L D + DV V GI S Sbjct: 414 DNFLHSGDLGIKDEDGNYRITGRIKDMIIRGGENIYPREIEEFLYKLDGVKDVQVAGIPS 473 Query: 479 ETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNP 538 + +G V +++ G + R + +K++ +K + V FV E P Sbjct: 474 KKYGEAVGAFIILQ------EGVEMHESDVR--DFCKNKISRYK-IPKYVFFVKEFPMTG 524 Query: 539 SGKILRRILK 548 SGKI + LK Sbjct: 525 SGKIQKFRLK 534 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: 654 Number of extensions: 30 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: 549 Length adjustment: 36 Effective length of query: 526 Effective length of database: 513 Effective search space: 269838 Effective search space used: 269838 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