Align ring 1,2-phenylacetyl-CoA epoxidase PaaA subunit (EC 1.14.13.149) (characterized)
to candidate GFF397 PGA1_c04080 phenylacetic acid degradation protein PaaA
Query= metacyc::MONOMER-15947 (330 letters) >FitnessBrowser__Phaeo:GFF397 Length = 325 Score = 467 bits (1201), Expect = e-136 Identities = 223/330 (67%), Positives = 267/330 (80%), Gaps = 6/330 (1%) Query: 1 MYAQLVETGVKRVKALEEMAPEERAFQERIDAEIKIEAKNWMPDAYRQTLIRQISQHAHS 60 MYAQ+V++ +A ++ + AFQ RIDA KIE K+WMP+ YR+TLIRQI QHAHS Sbjct: 1 MYAQMVKS-----EATQDDPEQLAAFQARIDAGEKIEPKDWMPEGYRKTLIRQIGQHAHS 55 Query: 61 EIVGMLPEGNWVTRAPTLKRKLQLMAKIQDEAGHGLYLYSAMETLGADRDEEIAKLHSGK 120 EIVG LPEGNW+TRAPTL+RK L+AK+QDEAGHGLYLY A ETLG RDE L G+ Sbjct: 56 EIVGQLPEGNWITRAPTLERKAILLAKVQDEAGHGLYLYCAAETLGVSRDEMTEMLLDGR 115 Query: 121 AKYSSIFNYPTLNWADMGAVGWLVDGAAIVNQVVLQRTSYGPYSRAMIRICKEESFHQRQ 180 KYSSIFNYPTLNWAD+GAVGWLVDGAAI+NQV LQRTS+GPYSRAMIR+CKEESFHQRQ Sbjct: 116 MKYSSIFNYPTLNWADIGAVGWLVDGAAIMNQVPLQRTSFGPYSRAMIRVCKEESFHQRQ 175 Query: 181 GYEILLTMMRHGTQAQKDMVQDAINRLWWPALMMFGPSDEHSPNSAQSMAWKIKRQSNDE 240 GY+ + M GT AQK M QDA+NRLW+P+LMMFGPSD+ S +SAQSMAWKIK +NDE Sbjct: 176 GYD-AIRKMAEGTPAQKKMAQDALNRLWYPSLMMFGPSDKDSVHSAQSMAWKIKMNTNDE 234 Query: 241 LRQRFIDQTVPQLELLGCTAPDPELKWNEERGHYDFGAIDWSEFYEVLKGNGPCNAERIA 300 LRQ+F+DQTVPQ E LG T PDP+LKWNEERGHYD+ DW+EF++V+KGNGPCN +R+A Sbjct: 235 LRQKFVDQTVPQAEYLGLTVPDPDLKWNEERGHYDYTDPDWNEFFDVIKGNGPCNVDRLA 294 Query: 301 TRRNAIDNGAWVREAAVAHARKQQHKRDAA 330 R A D+G WVR+ +AHA+K+ ++ AA Sbjct: 295 ARNKAWDDGEWVRDGLLAHAKKKAAQKHAA 324 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: 431 Number of extensions: 13 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: 325 Length adjustment: 28 Effective length of query: 302 Effective length of database: 297 Effective search space: 89694 Effective search space used: 89694 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: 48 (23.1 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