Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_013451021.1 CALNI_RS04490 phenylacetate--CoA ligase family protein
Query= SwissProt::P76085 (437 letters) >NCBI__GCF_000183405.1:WP_013451021.1 Length = 433 Score = 426 bits (1096), Expect = e-124 Identities = 206/427 (48%), Positives = 299/427 (70%), Gaps = 5/427 (1%) Query: 11 ETASVDELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDLRKFPCTTKQD 70 ET SVDE++ +Q +RL+ L Y+NV YR+KF G+ P+ + L D+ KFP T K D Sbjct: 9 ETLSVDEIKQIQLERLQSVLNRVYDNVTFYRKKFKEMGLEPESLKSLDDISKFPFTYKSD 68 Query: 71 LRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARSLRAAGGSPKD 130 LRDNYP+ FAVP+ +VRIH+SSGTTGKPTVVGYT+ND++NW N+VAR + A G + D Sbjct: 69 LRDNYPYGMFAVPLRDIVRIHSSSGTTGKPTVVGYTRNDLENWKNLVARIMVAGGVTAND 128 Query: 131 KIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDMIMVTPSYCLN 190 +H+A+ YGLFTGG G HY AE +GA+VIP+S G T++Q +++D++ +++ TPSY L+ Sbjct: 129 IVHIAFTYGLFTGGFGLHYAAEHIGASVIPVSSGNTKRQIMIMQDYRSSVLVCTPSYALH 188 Query: 191 LIEELERQLGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGITALDIYGLSEVMGPGVAM 250 + E L++ L + L+ + G+EPW + +R+E+ERRLG+ A D YGLSEVMGPGV+ Sbjct: 189 IAETLDK-LNLTKNDIHLKYALLGSEPWGEKIREEVERRLGVIATDNYGLSEVMGPGVSG 247 Query: 251 ECLETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVIRYRTRDLTRL 310 ECL +G + EDHFY EI++P PL +GE GEL+ TTLT+EA+P+IRYRTRD+TRL Sbjct: 248 ECL-YKNGLHVNEDHFYVEIIDPETCEPLPEGEKGELVITTLTREAMPLIRYRTRDITRL 306 Query: 311 LPG---TARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQLEVNRRGH 367 RT+ +M++ SGR+DDM+I+ GVN+FPSQ+EE + +F+ +PHY + V ++G Sbjct: 307 YRDKCPCGRTLIKMEKPSGRTDDMIIVNGVNIFPSQVEEVLKEFDQTTPHYMIFVKKKGR 366 Query: 368 LDSLSVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPRSEGKACR 427 LD L + +E+ E+ +++ + Q+ R+ +++GI + V +I R EGKA R Sbjct: 367 LDMLEIDIEMTEALFFDEMKKQKAILEQITERMFNVLGIKPAIKFVEPKTIERFEGKAKR 426 Query: 428 VFDLRNI 434 V DLRN+ Sbjct: 427 VIDLRNV 433 Lambda K H 0.320 0.137 0.411 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: 519 Number of extensions: 21 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: 437 Length of database: 433 Length adjustment: 32 Effective length of query: 405 Effective length of database: 401 Effective search space: 162405 Effective search space used: 162405 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