Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_011156793.1 TX73_RS06275 phenylacetate--CoA ligase
Query= BRENDA::B4EL89 (440 letters) >NCBI__GCF_000195775.1:WP_011156793.1 Length = 444 Score = 482 bits (1240), Expect = e-140 Identities = 243/427 (56%), Positives = 314/427 (73%), Gaps = 6/427 (1%) Query: 14 IETASRDELQALQLERLKWSLRHAYDNVPHYRRTFDAAGVHPDDLKSLADLAKFPFSTKN 73 IET R +L ALQ ERL+ + AY +VPHYR++FD AGV P DL SLADLAKFPF+ K Sbjct: 19 IETMPRPQLAALQFERLRKIVERAYRDVPHYRKSFDEAGVKPADLTSLADLAKFPFTKKT 78 Query: 74 DLRDNYPFGLFAVPREQVVRVHASSGTTGKPTVVGYTARDIDTWANVTARSIRAAGGRPG 133 DLRDNYPFG+FAVPR Q+ R+HASSGTTGKPTVVGYT D+D WAN+ ARS+ AG P Sbjct: 79 DLRDNYPFGMFAVPRNQMPRIHASSGTTGKPTVVGYTKTDLDNWANLMARSMVGAGASPD 138 Query: 134 DTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDFEPKIILVTPSYML 193 D +HNA+GYGLFTGGLG HYGAERLGC VVP SGG TE+QVQLI DF ++ TPSY L Sbjct: 139 DIVHNAYGYGLFTGGLGAHYGAERLGCTVVPASGGGTERQVQLIVDFGANVLCCTPSYAL 198 Query: 194 NLIDEMVRQGMDPAESSLKIGIFGAEPWTQALRNEVETRVGIDALDIYGLSEVMGPGVAC 253 N+ + + G+ ++ L++G+FGAEPW+ A+R ++E R+GI A+D+YGLSE+MGPGVAC Sbjct: 199 NIAEVAEQMGVSLKDAPLRVGLFGAEPWSDAMRRDLEARLGIKAVDVYGLSEIMGPGVAC 258 Query: 254 ECVETKDGPVIWEDHFYPEIIDPVTGEVLPDGSQGELVFTSLTKEAMPVIRYRTRDLTAL 313 EC ++G WEDHF E IDP T +VLP GS GELV T+LTKEA+P+IRYRTRD+T+L Sbjct: 259 ECHVAQNGLHGWEDHFLFETIDPETLQVLPMGSVGELVITTLTKEALPMIRYRTRDITSL 318 Query: 314 -LPPTA--RAMRRLAKITGRSDDMLIVRGVNVFPSQIEEIVVALPLLSGQFQITLSRDGH 370 P A R R+ ++TGR DDMLI+RGVNV+PSQ+E +++ P ++ +QI L+R+ Sbjct: 319 NTEPCACGRTHLRIMRVTGRDDDMLIIRGVNVYPSQVESVLIGFPGIAPHYQIVLTREKA 378 Query: 371 MDRLDLAVELRSEAAASVTDGERAALARELQHRIKTMVGVSSGVTVLAAGGIPATATGKA 430 +D + + VE+ A + D RA A E+ H IK+++GV+ V+V A G +P + GKA Sbjct: 379 LDAMTVEVEVAPGAPSD--DEARAKKAAEVTHHIKSLIGVTCKVSVKAPGEVP-RSQGKA 435 Query: 431 RRVIDRR 437 RV D+R Sbjct: 436 VRVKDQR 442 Lambda K H 0.319 0.136 0.400 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: 598 Number of extensions: 19 Number of successful extensions: 3 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: 440 Length of database: 444 Length adjustment: 32 Effective length of query: 408 Effective length of database: 412 Effective search space: 168096 Effective search space used: 168096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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