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 H281DRAFT_04144 H281DRAFT_04144 Tryptophan 2,3-dioxygenase holoenzyme /Tryptophan 2,3-dioxygenase apoenzyme
Query= SwissProt::Q1LK00 (299 letters) >FitnessBrowser__Burk376:H281DRAFT_04144 Length = 313 Score = 446 bits (1148), Expect = e-130 Identities = 212/297 (71%), Positives = 247/297 (83%), Gaps = 2/297 (0%) Query: 5 KGCPMGHG-AAPQNGDG-GDSGDTGNGWHGAQMDFARDMSYGDYLGLDQILSAQHPLSPD 62 +GCP GHG AAP + + G + +GWH AQ+DF+ MSYGDYL L +L AQHPLSPD Sbjct: 17 QGCPFGHGRAAPPSAEAPATEGASADGWHDAQLDFSESMSYGDYLSLGTVLDAQHPLSPD 76 Query: 63 HNEMLFIVQHQTTELWMKLMLHELRAARDGVKSDQLQPAFKMLARVSRIMDQLVQAWNVL 122 HNEMLFI+QHQT+ELWMKL L+ELRAA V D+L PAFKMLARVSRIM+QLVQAW+VL Sbjct: 77 HNEMLFIIQHQTSELWMKLALYELRAALGAVHRDELPPAFKMLARVSRIMEQLVQAWSVL 136 Query: 123 ATMTPPEYSAMRPYLGASSGFQSYQYREIEFILGNKNAAMLRPHAHRPEHLELVETALHT 182 ATMTP EY++MRPYLG+SSGFQSYQYR+IEF+LGNKN ML+PHAHR E L V+ +L + Sbjct: 137 ATMTPSEYTSMRPYLGSSSGFQSYQYRQIEFLLGNKNEQMLKPHAHRAEVLAEVKASLES 196 Query: 183 PSMYDEAIRLMARRGFQIDPEVVERDWTQPTQYNASVEAAWLEVYRNPSAHWELYELGEK 242 PS YDE ++L+ARRGF I P + RDWTQPT ++ASVEAAWLEVYRNPS HWELYE+ E+ Sbjct: 197 PSFYDEVVKLLARRGFAISPSRLTRDWTQPTVHDASVEAAWLEVYRNPSKHWELYEMAEE 256 Query: 243 FVDLEDAFRQWRFRHVTTVERVIGFKRGTGGTEGVSYLRRMLDVVLFPELWKLRTDL 299 VDLEDAFRQWRFRHVTTVER+IGFK+GTGGT G YLR+MLDVVLFPELW +RT L Sbjct: 257 LVDLEDAFRQWRFRHVTTVERIIGFKQGTGGTSGAPYLRKMLDVVLFPELWHVRTML 313 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: 387 Number of extensions: 5 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: 299 Length of database: 313 Length adjustment: 27 Effective length of query: 272 Effective length of database: 286 Effective search space: 77792 Effective search space used: 77792 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: 48 (23.1 bits)
Align candidate H281DRAFT_04144 H281DRAFT_04144 (Tryptophan 2,3-dioxygenase holoenzyme /Tryptophan 2,3-dioxygenase apoenzyme)
to HMM TIGR03036 (kynA: tryptophan 2,3-dioxygenase (EC 1.13.11.11))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR03036.hmm # target sequence database: /tmp/gapView.11063.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03036 [M=264] Accession: TIGR03036 Description: trp_2_3_diox: tryptophan 2,3-dioxygenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-136 439.3 0.5 2.7e-136 439.1 0.5 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04144 H281DRAFT_04144 Tryptophan 2,3-d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04144 H281DRAFT_04144 Tryptophan 2,3-dioxygenase holoenzyme /Tryptophan 2,3-di # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 439.1 0.5 2.7e-136 2.7e-136 1 264 [] 50 313 .] 50 313 .] 1.00 Alignments for each domain: == domain 1 score: 439.1 bits; conditional E-value: 2.7e-136 TIGR03036 1 dfsesmsYgdYlkldellsaqkplsedhdemlfivqhqvselwlklilheleaaaralradeleaa 66 dfsesmsYgdYl+l ++l+aq+pls+dh+emlfi+qhq+selw+kl+l+el+aa a+++del++a lcl|FitnessBrowser__Burk376:H281DRAFT_04144 50 DFSESMSYGDYLSLGTVLDAQHPLSPDHNEMLFIIQHQTSELWMKLALYELRAALGAVHRDELPPA 115 8***************************************************************** PP TIGR03036 67 lkalaRvsrileqlveaWdvLatltPaeysefRealgessGfqsyqyReiefllGnknaallkphe 132 +k+laRvsri+eqlv+aW+vLat+tP+ey+++R++lg+ssGfqsyqyR+iefllGnkn+++lkph+ lcl|FitnessBrowser__Burk376:H281DRAFT_04144 116 FKMLARVSRIMEQLVQAWSVLATMTPSEYTSMRPYLGSSSGFQSYQYRQIEFLLGNKNEQMLKPHA 181 ****************************************************************** PP TIGR03036 133 kdpellaeleaaleePslYdevlrllarrGfaipaevlerdvtkpaeaneeveaawlevYrdaeke 198 +++e+lae++a+le+Ps+Ydev++llarrGfai ++l rd+t+p+ ++++veaawlevYr+++k+ lcl|FitnessBrowser__Burk376:H281DRAFT_04144 182 HRAEVLAEVKASLESPSFYDEVVKLLARRGFAISPSRLTRDWTQPTVHDASVEAAWLEVYRNPSKH 247 ****************************************************************** PP TIGR03036 199 welyelaeklvDledlfrrWRfrhlttveRiiGfkrGtGGssGvayLkkaldvelfPelwkvRtel 264 welye+ae+lvDled+fr+WRfrh+ttveRiiGfk+GtGG+sG+ yL+k+ldv+lfPelw+vRt l lcl|FitnessBrowser__Burk376:H281DRAFT_04144 248 WELYEMAEELVDLEDAFRQWRFRHVTTVERIIGFKQGTGGTSGAPYLRKMLDVVLFPELWHVRTML 313 ***************************************************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (264 nodes) Target sequences: 1 (313 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8.18 // [ok]
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