Align subunit of catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate PP_3166 PP_3166 catechol 1,2-dioxygenase
Query= metacyc::MONOMER-3422 (311 letters) >FitnessBrowser__Putida:PP_3166 Length = 304 Score = 461 bits (1187), Expect = e-135 Identities = 233/322 (72%), Positives = 255/322 (79%), Gaps = 31/322 (9%) Query: 1 MTVKISHTADVQAFFNKVAGLDHAEGNPRFKQIILRVLQDTARLVEDLEITEDEFWHAID 60 MTV ISHTA+VQ FF + AG +A GNPR K+I+ R+LQDTARL+EDL+I+EDEFWHA+D Sbjct: 1 MTVNISHTAEVQQFFEQAAGFCNAAGNPRLKRIVQRLLQDTARLIEDLDISEDEFWHAVD 60 Query: 61 YLNRLGGRNEAGLLAAGLGIEHFLDLLQDAKDAEAGLGGGTPRTIEGPLYVAGAPLAQGE 120 YLNRLGGR EAGLL AGLGIEHFLDLLQDAKD EAG GGTPRTIEGPLYVAGAP+AQGE Sbjct: 61 YLNRLGGRGEAGLLVAGLGIEHFLDLLQDAKDQEAGRVGGTPRTIEGPLYVAGAPIAQGE 120 Query: 121 ARMDDGTDPGV--VMFLQGQVFDADGKPLAGATVDLWHANTQGTYSYFDSTQSEYNLRRR 178 RMDDG++ GV VMFL+GQV D G+PL GATVDLWHANT+GTYS+FD +QS YNLRRR Sbjct: 121 VRMDDGSEEGVATVMFLEGQVLDPHGRPLPGATVDLWHANTRGTYSFFDQSQSAYNLRRR 180 Query: 179 IITDAVGRYRARSIVPSGYGCDPQGTTQECLDLLGRHGQRPAHVHFFISAPGFRHLTTQI 238 I+TDA GRYRARSIVPSGYGCDPQG TQECLDLLGRHGQRPAHVHFFISAPG+RHLTTQI Sbjct: 181 IVTDAQGRYRARSIVPSGYGCDPQGPTQECLDLLGRHGQRPAHVHFFISAPGYRHLTTQI 240 Query: 239 NLKMPLPRVIAVFRASALPNCEGDKYLWDDFAYATRDGLIGELRFV----------AFDF 288 NL GDKYLWDDFAYATRDGL+GE+ FV FDF Sbjct: 241 NL-------------------SGDKYLWDDFAYATRDGLVGEVVFVEGPDGRHAELKFDF 281 Query: 289 HLQAAAAPEAEARSHRPRALQE 310 LQ A E RS RPRALQE Sbjct: 282 QLQQAQGGADEQRSGRPRALQE 303 Lambda K H 0.321 0.139 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: 439 Number of extensions: 20 Number of successful extensions: 4 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: 311 Length of database: 304 Length adjustment: 27 Effective length of query: 284 Effective length of database: 277 Effective search space: 78668 Effective search space used: 78668 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate PP_3166 PP_3166 (catechol 1,2-dioxygenase)
to HMM TIGR02439 (catA: catechol 1,2-dioxygenase (EC 1.13.11.1))
# 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/TIGR02439.hmm # target sequence database: /tmp/gapView.30198.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02439 [M=285] Accession: TIGR02439 Description: catechol_proteo: catechol 1,2-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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-142 457.9 0.0 6.4e-142 457.6 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_3166 PP_3166 catechol 1,2-dioxygenase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3166 PP_3166 catechol 1,2-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.6 0.0 6.4e-142 6.4e-142 2 268 .. 8 274 .. 7 284 .. 0.97 Alignments for each domain: == domain 1 score: 457.6 bits; conditional E-value: 6.4e-142 TIGR02439 2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgllaaGlGleh 76 t+evq++++++ag+ ++ gn+r k+iv+r+l+d++++iedldi+edefw+av+yln+lG ++e+gll+aGlG+eh lcl|FitnessBrowser__Putida:PP_3166 8 TAEVQQFFEQAAGFCNAAGNPRLKRIVQRLLQDTARLIEDLDISEDEFWHAVDYLNRLGGRGEAGLLVAGLGIEH 82 78************************************************************************* PP TIGR02439 77 fldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvldaeGkpiagakvevw 151 fldl++da+d++ag+ ggtPrtieGPlyvaGap+++G+ r+ddgse+ a++++l+Gqvld +G+p++ga+v++w lcl|FitnessBrowser__Putida:PP_3166 83 FLDLLQDAKDQEAGRVGGTPRTIEGPLYVAGAPIAQGEVRMDDGSEEGVATVMFLEGQVLDPHGRPLPGATVDLW 157 *************************************************************************** PP TIGR02439 152 hanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnllGrhGerPahvhffvsapg 226 han++G+ysffd+sqs +nlrr+i+tda+G+yrars+vP+Gyg++pqgptq++l+llGrhG+rPahvhff+sapg lcl|FitnessBrowser__Putida:PP_3166 158 HANTRGTYSFFDQSQSAYNLRRRIVTDAQGRYRARSIVPSGYGCDPQGPTQECLDLLGRHGQRPAHVHFFISAPG 232 *************************************************************************** PP TIGR02439 227 yrklttqinlegdkylyddfafatreglvaevkevedaaaak 268 yr+lttqinl+gdkyl+ddfa+atr+glv+ev +ve+ + + lcl|FitnessBrowser__Putida:PP_3166 233 YRHLTTQINLSGDKYLWDDFAYATRDGLVGEVVFVEGPDGRH 274 **********************************99876554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (304 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.58 // [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