Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_022603146.1 NSB1T_RS28555 AMP-binding protein
Query= BRENDA::A7KUK6 (562 letters) >NCBI__GCF_000473955.1:WP_022603146.1 Length = 550 Score = 167 bits (423), Expect = 1e-45 Identities = 149/563 (26%), Positives = 256/563 (45%), Gaps = 60/563 (10%) Query: 14 EVDLWTFLFERKDRAYPDDKIIYQDADTQRHYTYKSLRDASLDFGKGLKALYEWRKGDVL 73 E L FL ++ + I+Y D D + +TY + KG+ A+ K + Sbjct: 5 EKTLGDFLEYWAEKTPDKEFIVYSDRDLR--FTYSEFNKRVNNLAKGMMAIGV-EKDSKV 61 Query: 74 ALFTPNSIDTPVVMWGTLWAGGTISPANPGYTVDELAFQLKNSHAKGLVTQA-------- 125 ++ N D ++ + G + N Y EL + ++N+ L Sbjct: 62 GIWATNVPDWLTFLFASAKIGAILVTVNTNYKQHELEYLVENADIHTLCISNGTFDSDYV 121 Query: 126 ----SVLPVAREAA----KKVGMPEDR-IILIGDQRDPDARVKHFTSVRNISGAT----- 171 ++LP + + K P R ++ IG ++ R + T+ + G T Sbjct: 122 DMTYTMLPELKTSQRGHLKSNKFPYMRNVVYIGQEKH---RGMYNTAELLLLGNTITDEK 178 Query: 172 -RYRKQKITPAKDVAFLVYSSGTTGVPKGVMISHRNIVANIRQQFIAEGEMLSWNGGPDG 230 +KQK DV + Y+SGTTG PKGVM++H NI N G+ + ++ Sbjct: 179 LETQKQKFN-CYDVVNMQYTSGTTGFPKGVMLTHHNITNN----GYCIGQCMKFS----- 228 Query: 231 KGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMSKFDIEKWCAHVQNYRCSFSYIVPPV 290 + DRV +P +H +G+ I + G +++ +FD A V RC+ Y VP + Sbjct: 229 ENDRVCLPVPLFHCFGIVLGIMAIITNGGCAVMLERFDPLVVLASVHKERCTALYGVPTM 288 Query: 291 VLLLGKHPVVDKYDLSSLR--MMNSGAAP--LTQELVEAVYSRIKVGIKQGYGLSETSPT 346 + HP+ +DLSSLR +M P L +E+++ +Y + I YGL+ETSP Sbjct: 289 FIAELNHPMFSMFDLSSLRTGIMAGSLCPEWLMREVMDKMYMK---EITSVYGLTETSPG 345 Query: 347 THSQRWEDWREAMGS-VGRLMPNMQAKYMTMPEDGSEPKEVGEGEVGELYLKGPNVFLGY 405 + +D E S VG +P ++ + + D +E G GE+ +G N+ GY Sbjct: 346 MTQSKVDDPVEVRASTVGSDLPGVEVRVI----DPETLEECPVGVQGEMCCRGYNIMKGY 401 Query: 406 HENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKELIKYKGFQVPPAELEGYLVDN 465 ++ PEAT + ++G+ +GD+G + +GN+ IT R+K++I G + P E+E +L Sbjct: 402 YKMPEATAAIIDKNGFLHSGDLGIKTPEGNYKITGRIKDMIIRGGENIYPREIEEFLYQI 461 Query: 466 DAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEKDEAARIIKWLDSKVASHKRLR 525 I DV V + S+ +G EV +++ +S + + K++ HK + Sbjct: 462 PQIKDVQVAAVPSKKYGEEVGAFIILKEGESLHD--------CDVKDFCKGKISRHK-IP 512 Query: 526 GGVHFVDEIPKNPSGKILRRILK 548 + F+D+ P SGKI + LK Sbjct: 513 KYIFFIDQFPLTGSGKIQKYKLK 535 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: 700 Number of extensions: 37 Number of successful extensions: 5 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: 550 Length adjustment: 36 Effective length of query: 526 Effective length of database: 514 Effective search space: 270364 Effective search space used: 270364 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 24 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