Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_067075177.1 MCUHO_RS05970 phenylacetate--CoA ligase
Query= BRENDA::B4EL89 (440 letters) >NCBI__GCF_001602375.1:WP_067075177.1 Length = 429 Score = 390 bits (1002), Expect = e-113 Identities = 204/426 (47%), Positives = 283/426 (66%), Gaps = 8/426 (1%) Query: 14 IETASRDELQALQLERLKWSLRHAYDNVPHYRRTFDAAGVHPDDLKSLADLAKFPFSTKN 73 +ET EL LQL+RLKWSL A V Y+R AG+ PDD+K+L D+ K PF+ K Sbjct: 7 METIRSSELADLQLKRLKWSLAQA-QKVGLYQRKLKEAGISPDDIKTLDDVEKLPFTYKK 65 Query: 74 DLRDNYPFGLFAVPREQVVRVHASSGTTGKPTVVGYTARDIDTWANVTARSIRAAGGRPG 133 +L+ YPFGLFAVP +++VR+H +SGTTGKPTVVGYT +D+D W+ + AR++ G Sbjct: 66 ELQAGYPFGLFAVPLKEIVRIHTTSGTTGKPTVVGYTRQDLDNWSELIARNMTMIGLGED 125 Query: 134 DTLHNAFGYGLFTGGLGIHYGAERLGCMVVPMSGGQTEKQVQLIRDFEPKIILVTPSYML 193 D NA YGLFTGGLG HYGAE++G V+P + G T +Q+++I DF + TPSY L Sbjct: 126 DVFQNAVNYGLFTGGLGFHYGAEKIGMTVIPSATGNTRRQIEMIEDFGVTALHCTPSYAL 185 Query: 194 NLIDEMVRQGMDPAESSLKIGIFGAEPWTQALRNEVETRVGIDALDIYGLSEVMGPGVAC 253 +L + V + M +LK GIFGAEPW++++RNE+E R+G+ A D YGLSE+ GPGVA Sbjct: 186 HLAE--VAESMGKTLDTLKTGIFGAEPWSESMRNELERRLGVKAYDSYGLSEMYGPGVAF 243 Query: 254 ECVETKDGPVIWEDHFYPEIIDPVTGEVLPDGSQGELVFTSLTKEAMPVIRYRTRDLTAL 313 EC E +DG IW D + EIIDP TGE L G +GELV T L K A+P++RYRT D+T L Sbjct: 244 ECPE-RDGLHIWHDCYLVEIIDPKTGERLAPGERGELVITPLVKNALPLVRYRTGDVTRL 302 Query: 314 LPPTARAMR--RLAKITGRSDDMLIVRGVNVFPSQIEEIVVALPLLSGQFQITLSRDGHM 371 + R ++ +ITGRSDDML++RG+NVFPSQIE ++ ALP + QF + + R H+ Sbjct: 303 MDDGCVCGRGQKIERITGRSDDMLVIRGINVFPSQIEHVLRALPEVGEQFIVYIDRVKHL 362 Query: 372 DRLDLAVELRSEAAASVTDGERAALARELQHRIKTMVGVSSGVTVLAAGGIPATATGKAR 431 D + + VE+ S A S + A + +++ + ++G+ + V ++ G +P GKA+ Sbjct: 363 DEMTIEVEM-SRAGFSGELQDLARMQKKISGELHNILGLRTAVKLVEPGALP-RFEGKAK 420 Query: 432 RVIDRR 437 RVIDRR Sbjct: 421 RVIDRR 426 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: 570 Number of extensions: 24 Number of successful extensions: 6 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: 429 Length adjustment: 32 Effective length of query: 408 Effective length of database: 397 Effective search space: 161976 Effective search space used: 161976 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