Align subunit of catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate PP_3713 PP_3713 catechol 1,2-dioxygenase
Query= metacyc::MONOMER-3422 (311 letters) >FitnessBrowser__Putida:PP_3713 Length = 311 Score = 549 bits (1414), Expect = e-161 Identities = 276/330 (83%), Positives = 284/330 (86%), Gaps = 38/330 (11%) Query: 1 MTVKISHTADVQAFFNKVAGLDHAEGNPRFKQIILRVLQDTARLVEDLEITEDEFWHAID 60 MTVKISHTAD+QAFFN+VAGLDHAEGNPRFKQIILRVLQDTARL+EDLEITEDEFWHA+D Sbjct: 1 MTVKISHTADIQAFFNRVAGLDHAEGNPRFKQIILRVLQDTARLIEDLEITEDEFWHAVD 60 Query: 61 YLNRLGGRNEAGLLAAGLGIEHFLDLLQDAKDAEAGLGGGTPRTIEGPLYVAGAPLAQGE 120 YLNRLGGRNEAGLLAAGLGIEHFLDLLQDAKDAEAGLGGGTPRTIEGPLYVAGAPLAQGE Sbjct: 61 YLNRLGGRNEAGLLAAGLGIEHFLDLLQDAKDAEAGLGGGTPRTIEGPLYVAGAPLAQGE 120 Query: 121 ARMDDGTDPGVVMFLQGQVFDADGKPLAGATVDLWHANTQGTYSYFDSTQSEYNLRRRII 180 ARMDDGTDPGVVMFLQGQVFDADGKPLAGATVDLWHANTQGTYSYFDSTQSE+NLRRRII Sbjct: 121 ARMDDGTDPGVVMFLQGQVFDADGKPLAGATVDLWHANTQGTYSYFDSTQSEFNLRRRII 180 Query: 181 TDAVGRYRARSIVPSGYGCDPQGTTQECLDLLGRHGQRPAHVHFFISAPGFRHLTTQINL 240 TDA GRYRARSIVPSGYGCDPQG TQECLDLLGRHGQRPAHVHFFISAPG RHLTTQIN Sbjct: 181 TDAEGRYRARSIVPSGYGCDPQGPTQECLDLLGRHGQRPAHVHFFISAPGHRHLTTQINF 240 Query: 241 KMPLPRVIAVFRASALPNCEGDKYLWDDFAYATRDGLIGELRFV---------------- 284 GDKYLWDDFAYATRDGLIGELRFV Sbjct: 241 -------------------AGDKYLWDDFAYATRDGLIGELRFVEDAAAARDRGVQGERF 281 Query: 285 ---AFDFHLQAAAAPEAEARSHRPRALQEG 311 +FDF LQ A +P+AEARSHRPRALQEG Sbjct: 282 AELSFDFRLQGAKSPDAEARSHRPRALQEG 311 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: 502 Number of extensions: 15 Number of successful extensions: 3 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: 311 Length adjustment: 27 Effective length of query: 284 Effective length of database: 284 Effective search space: 80656 Effective search space used: 80656 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_3713 PP_3713 (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.2707.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-154 496.9 0.1 7.7e-154 496.7 0.1 1.0 1 lcl|FitnessBrowser__Putida:PP_3713 PP_3713 catechol 1,2-dioxygenase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3713 PP_3713 catechol 1,2-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 496.7 0.1 7.7e-154 7.7e-154 2 285 .] 8 290 .. 7 290 .. 0.99 Alignments for each domain: == domain 1 score: 496.7 bits; conditional E-value: 7.7e-154 TIGR02439 2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgllaaGlGleh 76 t+++qa++++vagl++++gn+r+kqi+lrvl+d++++iedl+itedefw+av+yln+lG +ne+gllaaGlG+eh lcl|FitnessBrowser__Putida:PP_3713 8 TADIQAFFNRVAGLDHAEGNPRFKQIILRVLQDTARLIEDLEITEDEFWHAVDYLNRLGGRNEAGLLAAGLGIEH 82 789************************************************************************ PP TIGR02439 77 fldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvldaeGkpiagakvevw 151 fldl++da+da+agl ggtPrtieGPlyvaGap+++G+ar+ddg+ d + +++l+Gqv+da+Gkp+aga+v++w lcl|FitnessBrowser__Putida:PP_3713 83 FLDLLQDAKDAEAGLGGGTPRTIEGPLYVAGAPLAQGEARMDDGT--DPGVVMFLQGQVFDADGKPLAGATVDLW 155 *********************************************..668************************* PP TIGR02439 152 hanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnllGrhGerPahvhffvsapg 226 han++G+ys+fd++qsefnlrr+iitdaeG+yrars+vP+Gyg++pqgptq++l+llGrhG+rPahvhff+sapg lcl|FitnessBrowser__Putida:PP_3713 156 HANTQGTYSYFDSTQSEFNLRRRIITDAEGRYRARSIVPSGYGCDPQGPTQECLDLLGRHGQRPAHVHFFISAPG 230 *************************************************************************** PP TIGR02439 227 yrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgveg.rfaeiefdlel 285 +r+lttqin++gdkyl+ddfa+atr+gl++e+++vedaaaa++rgv+g rfae++fd++l lcl|FitnessBrowser__Putida:PP_3713 231 HRHLTTQINFAGDKYLWDDFAYATRDGLIGELRFVEDAAAARDRGVQGeRFAELSFDFRL 290 ***********************************************989*******987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (311 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: 00:00:00.01 # Mc/sec: 7.39 // [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