Align ring 1,2-phenylacetyl-CoA epoxidase PaaA subunit (EC 1.14.13.149) (characterized)
to candidate RR42_RS23725 RR42_RS23725 phenylacetate-CoA oxygenase
Query= metacyc::MONOMER-15947 (330 letters) >FitnessBrowser__Cup4G11:RR42_RS23725 Length = 334 Score = 452 bits (1163), Expect = e-132 Identities = 209/306 (68%), Positives = 258/306 (84%), Gaps = 1/306 (0%) Query: 18 EMAPEERAFQERIDAEIKIEAKNWMPDAYRQTLIRQISQHAHSEIVGMLPEGNWVTRAPT 77 +++PE+ F +DA+ KIEA++WMPDAYR+TLIRQISQHAHSEI+GM PEGNW++RAP+ Sbjct: 21 DVSPEQAHFDAVMDADGKIEAQDWMPDAYRKTLIRQISQHAHSEIIGMQPEGNWISRAPS 80 Query: 78 LKRKLQLMAKIQDEAGHGLYLYSAMETLGADRDEEIAKLHSGKAKYSSIFNYPTLNWADM 137 LKRK L+AK+QDE GHGLYLYSA ET+G RD+ + LH+GKAKYSSIFNYPT WAD+ Sbjct: 81 LKRKAILLAKVQDEGGHGLYLYSAAETMGVSRDQLVDALHAGKAKYSSIFNYPTPTWADV 140 Query: 138 GAVGWLVDGAAIVNQVVLQRTSYGPYSRAMIRICKEESFHQRQGYEILLTMMRHGTQAQK 197 G +GWLVDGAAI+NQ+ L R +YGPY+RAMIRICKEESFHQRQG++ LL+MM+ GTQAQK Sbjct: 141 GVIGWLVDGAAIMNQIPLCRCTYGPYARAMIRICKEESFHQRQGFDALLSMMK-GTQAQK 199 Query: 198 DMVQDAINRLWWPALMMFGPSDEHSPNSAQSMAWKIKRQSNDELRQRFIDQTVPQLELLG 257 DMVQ+++NR WWP LMMFGPSD+ S +S QS W IKR SND+LRQ+F+D TV Q ++LG Sbjct: 200 DMVQESVNRWWWPVLMMFGPSDKDSIHSGQSFKWGIKRISNDDLRQKFVDATVEQAKILG 259 Query: 258 CTAPDPELKWNEERGHYDFGAIDWSEFYEVLKGNGPCNAERIATRRNAIDNGAWVREAAV 317 T PDP+LKWNE RG +D+GAIDW EF+ V+ G+GPCN ER+ATR A ++GAWVREAA+ Sbjct: 260 VTLPDPDLKWNEARGAHDYGAIDWEEFWRVVNGDGPCNKERLATRVKAHNDGAWVREAAL 319 Query: 318 AHARKQ 323 AHA KQ Sbjct: 320 AHAEKQ 325 Lambda K H 0.318 0.131 0.402 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: 436 Number of extensions: 10 Number of successful extensions: 2 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: 330 Length of database: 334 Length adjustment: 28 Effective length of query: 302 Effective length of database: 306 Effective search space: 92412 Effective search space used: 92412 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: 49 (23.5 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