Align Tryptophan 2,3-dioxygenase; TDO; Tryptamin 2,3-dioxygenase; Tryptophan oxygenase; TO; TRPO; Tryptophan pyrrolase; Tryptophanase; EC 1.13.11.11 (characterized)
to candidate CCNA_02980 CCNA_02980 tryptophan 2,3-dioxygenase
Query= SwissProt::Q1LK00 (299 letters) >FitnessBrowser__Caulo:CCNA_02980 Length = 263 Score = 278 bits (712), Expect = 7e-80 Identities = 136/262 (51%), Positives = 183/262 (69%) Query: 38 ARDMSYGDYLGLDQILSAQHPLSPDHNEMLFIVQHQTTELWMKLMLHELRAARDGVKSDQ 97 A+DM+Y YL LD++LSAQ PLS H+E+LFIV HQT ELW+K +LHE+ A + Sbjct: 2 AQDMTYARYLALDELLSAQKPLSDRHDELLFIVIHQTKELWLKEILHEVALALKLIAGGD 61 Query: 98 LQPAFKMLARVSRIMDQLVQAWNVLATMTPPEYSAMRPYLGASSGFQSYQYREIEFILGN 157 ++PA+K LARVSRI + +W++LATMTP +Y + R LG SSGFQS+Q+R +E++LG Sbjct: 62 VEPAYKALARVSRIQTVMTLSWDILATMTPADYLSFRDDLGTSSGFQSHQFRALEYLLGL 121 Query: 158 KNAAMLRPHAHRPEHLELVETALHTPSMYDEAIRLMARRGFQIDPEVVERDWTQPTQYNA 217 K+ + L+ H RPE L ++++AL +PS+YD AI + R G + + RD++Q + Sbjct: 122 KDQSFLKFHTERPEALAMLKSALESPSLYDVAIAQLPRHGLTVPDAALHRDFSQTYVPSP 181 Query: 218 SVEAAWLEVYRNPSAHWELYELGEKFVDLEDAFRQWRFRHVTTVERVIGFKRGTGGTEGV 277 VEAAWLEVYR+P +WELY+L EK VDL+DA WR +HV TVER+IG + GTGGT+GV Sbjct: 182 EVEAAWLEVYRDPKRYWELYQLAEKLVDLDDALVTWRHKHVLTVERIIGGRPGTGGTDGV 241 Query: 278 SYLRRMLDVVLFPELWKLRTDL 299 YL L FPELW LRT L Sbjct: 242 GYLASTLRRRAFPELWSLRTKL 263 Lambda K H 0.321 0.136 0.424 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: 265 Number of extensions: 9 Number of successful extensions: 1 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: 299 Length of database: 263 Length adjustment: 26 Effective length of query: 273 Effective length of database: 237 Effective search space: 64701 Effective search space used: 64701 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: 47 (22.7 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