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 GFF980 PGA1_c09970 tryptophan 2,3-dioxygenase KynA
Query= SwissProt::Q1LK00 (299 letters) >FitnessBrowser__Phaeo:GFF980 Length = 277 Score = 340 bits (872), Expect = 2e-98 Identities = 169/268 (63%), Positives = 207/268 (77%), Gaps = 1/268 (0%) Query: 32 GAQMDFARDMSYGDYLGLDQILSAQHPLSPDHNEMLFIVQHQTTELWMKLMLHELRAARD 91 GAQM F MSYGDYL LD +L+AQ + H+EMLFI+QHQT+ELWM+L +HEL AAR Sbjct: 11 GAQMSFDGRMSYGDYLSLDLLLNAQKTWTNTHDEMLFIIQHQTSELWMRLAIHELTAARS 70 Query: 92 GVKSDQLQPAFKMLARVSRIMDQLVQAWNVLATMTPPEYSAMRPYLGASSGFQSYQYREI 151 + +++ AFKMLARV+RI +QL AW+VL TMTP +YSA R LG SSGFQS+QYR+I Sbjct: 71 RLLANKPHEAFKMLARVARIFEQLNSAWDVLRTMTPSDYSAFRDELGQSSGFQSHQYRQI 130 Query: 152 EFILGNKNAAMLRPHAHRPEHLELVETALHTPSMYDEAIRLMARRGFQIDPEVVERDWTQ 211 EF+LGN+N AMLRPHAHRP+ L L+E L PS+YD A++ + +R F + EV+ R+ ++ Sbjct: 131 EFMLGNRNKAMLRPHAHRPDVLALLEDELSQPSLYDVALKTLGQR-FDLPKEVLNRNLSE 189 Query: 212 PTQYNASVEAAWLEVYRNPSAHWELYELGEKFVDLEDAFRQWRFRHVTTVERVIGFKRGT 271 + +VEAAW EVYRN AHW+LYEL EK VD ED FR+WRF HVTTVERVIGFKRGT Sbjct: 190 AYTPHPAVEAAWSEVYRNTEAHWDLYELAEKLVDFEDYFRRWRFNHVTTVERVIGFKRGT 249 Query: 272 GGTEGVSYLRRMLDVVLFPELWKLRTDL 299 GGT GVSYL+RML+V LFPELW LRT L Sbjct: 250 GGTGGVSYLKRMLEVELFPELWHLRTAL 277 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: 313 Number of extensions: 8 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: 277 Length adjustment: 26 Effective length of query: 273 Effective length of database: 251 Effective search space: 68523 Effective search space used: 68523 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)
Align candidate GFF980 PGA1_c09970 (tryptophan 2,3-dioxygenase KynA)
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.6144.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-126 406.8 1.3 2.2e-126 406.7 1.3 1.0 1 lcl|FitnessBrowser__Phaeo:GFF980 PGA1_c09970 tryptophan 2,3-dioxy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF980 PGA1_c09970 tryptophan 2,3-dioxygenase KynA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.7 1.3 2.2e-126 2.2e-126 1 264 [] 15 277 .] 15 277 .] 0.99 Alignments for each domain: == domain 1 score: 406.7 bits; conditional E-value: 2.2e-126 TIGR03036 1 dfsesmsYgdYlkldellsaqkplsedhdemlfivqhqvselwlklilheleaaaralradeleaalkalaRvsril 77 +f+ +msYgdYl+ld ll+aqk+ ++ hdemlfi+qhq+selw++l++hel+aa++ l a++ ++a+k+laRv+ri+ lcl|FitnessBrowser__Phaeo:GFF980 15 SFDGRMSYGDYLSLDLLLNAQKTWTNTHDEMLFIIQHQTSELWMRLAIHELTAARSRLLANKPHEAFKMLARVARIF 91 599************************************************************************** PP TIGR03036 78 eqlveaWdvLatltPaeysefRealgessGfqsyqyReiefllGnknaallkphekdpellaeleaaleePslYdev 154 eql++aWdvL+t+tP++ys+fR++lg+ssGfqs qyR+ief+lGn+n+a+l+ph+++p++la le++l++PslYd++ lcl|FitnessBrowser__Phaeo:GFF980 92 EQLNSAWDVLRTMTPSDYSAFRDELGQSSGFQSHQYRQIEFMLGNRNKAMLRPHAHRPDVLALLEDELSQPSLYDVA 168 ***************************************************************************** PP TIGR03036 155 lrllarrGfaipaevlerdvtkpaeaneeveaawlevYrdaekewelyelaeklvDledlfrrWRfrhlttveRiiG 231 l+ l +r f++p+evl+r+++++++ +++veaaw evYr++e++w+lyelaeklvD+ed+frrWRf+h+ttveR+iG lcl|FitnessBrowser__Phaeo:GFF980 169 LKTLGQR-FDLPKEVLNRNLSEAYTPHPAVEAAWSEVYRNTEAHWDLYELAEKLVDFEDYFRRWRFNHVTTVERVIG 244 ****977.********************************************************************* PP TIGR03036 232 fkrGtGGssGvayLkkaldvelfPelwkvRtel 264 fkrGtGG+ Gv+yLk++l+velfPelw++Rt l lcl|FitnessBrowser__Phaeo:GFF980 245 FKRGTGGTGGVSYLKRMLEVELFPELWHLRTAL 277 *******************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (264 nodes) Target sequences: 1 (277 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 8.46 // [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