Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate Echvi_2513 Echvi_2513 Phenylalanine-4-hydroxylase
Query= reanno::pseudo5_N2C3_1:AO356_03975 (261 letters) >FitnessBrowser__Cola:Echvi_2513 Length = 264 Score = 187 bits (475), Expect = 2e-52 Identities = 96/238 (40%), Positives = 142/238 (59%), Gaps = 6/238 (2%) Query: 2 KQTQYVAREPDA----QGFIHYTAEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPH 57 K ++V +P Q + YT E AVW TL RQ+ + A + YL+GI ++ Sbjct: 4 KSAEWVFEDPRLKAMHQDYDAYTEENFAVWKTLYERQIVNLPNAASKAYLEGIKEINFTA 63 Query: 58 DRIPQLDEINKVLGQTTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEP 117 DRI E+N++L ++TGW V VP LI FF LL K+FP +T++R E+LDYL+EP Sbjct: 64 DRIANFSEVNQILSKSTGWGVQVVPGLIDDDLFFGLLNHKRFPSSTWLRKMEQLDYLEEP 123 Query: 118 DIFHEIFGHCPLLTNPWFAEFTHTYGKLGLQASKEERV--YLARLYWMTIEFGLVQTPQG 175 D+FH+ F H P+LTN + +F + L+ ++ L+R+YW TIEFGL++ Sbjct: 124 DMFHDAFAHMPMLTNQPYVDFLQDLSGIALKYIDDKWAIHLLSRIYWFTIEFGLIRENGA 183 Query: 176 RRIYGGGILSSPKETVYCLSDEPEHQAFDPLEAMRTPYRIDILQPVYFVLPELKRLFD 233 +IYG GILSS ET + LSD+PEH+ +D M+TPY D Q Y+V+ ++L++ Sbjct: 184 LKIYGAGILSSAGETKFSLSDDPEHRDYDVRSIMQTPYWKDKFQDKYYVIESYEQLYN 241 Lambda K H 0.323 0.141 0.439 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: 202 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: 261 Length of database: 264 Length adjustment: 25 Effective length of query: 236 Effective length of database: 239 Effective search space: 56404 Effective search space used: 56404 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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