Align catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate HSERO_RS06545 HSERO_RS06545 catechol 1,2-dioxygenase
Query= BRENDA::P07773 (311 letters) >FitnessBrowser__HerbieS:HSERO_RS06545 Length = 311 Score = 496 bits (1276), Expect = e-145 Identities = 230/310 (74%), Positives = 267/310 (86%) Query: 1 MEVKIFNTQDVQDFLRVASGLEQEGGNPRVKQIIHRVLSDLYKAIEDLNITSDEYWAGVA 60 M KIF+T++VQDFLR+ASGL+ EGGNPR KQI+HR+LSDL+K IEDL ITSDEYWAGVA Sbjct: 1 MAAKIFSTREVQDFLRLASGLDTEGGNPRTKQIVHRILSDLFKTIEDLEITSDEYWAGVA 60 Query: 61 YLNQLGANQEAGLLSPGLGFDHYLDMRMDAEDAALGIENATPRTIEGPLYVAGAPESVGY 120 Y+N+LG EAGLLSPGLG D +LDMRMDAEDAALGI TPRTIEGPLYVAGAP G+ Sbjct: 61 YINRLGTAHEAGLLSPGLGLDRFLDMRMDAEDAALGIAGGTPRTIEGPLYVAGAPVEQGF 120 Query: 121 ARMDDGSDPNGHTLILHGTIFDADGKPLPNAKVEIWHANTKGFYSHFDPTGEQQAFNMRR 180 AR+DDGSD +G T+I+HGT++ ADGKP+P A+VE+WHANTKGFYSHFDPTGEQ+ FNMRR Sbjct: 121 ARLDDGSDKSGQTIIMHGTVYGADGKPMPGAQVEVWHANTKGFYSHFDPTGEQKPFNMRR 180 Query: 181 SIITDENGQYRVRTILPAGYGCPPEGPTQQLLNQLGRHGNRPAHIHYFVSADGHRKLTTQ 240 +IITD G+Y+ R+I+P YGCPP GPTQ LLN LGRHGNRPAHIH+FV+A+GHRKLTTQ Sbjct: 181 TIITDAQGRYKFRSIMPTAYGCPPAGPTQGLLNALGRHGNRPAHIHFFVTAEGHRKLTTQ 240 Query: 241 INVAGDPYTYDDFAYATREGLVVDAVEHTDPEAIKANDVEGPFAEMVFDLKLTRLVDGVD 300 IN+ GDP YDDFAYATREGLV VE TD +IKA +EGPFAE+VFD+KLT LV+G D Sbjct: 241 INIEGDPLIYDDFAYATREGLVPPLVERTDAASIKAEGLEGPFAEIVFDIKLTSLVNGAD 300 Query: 301 NQVVDRPRLA 310 NQ+VDRPRLA Sbjct: 301 NQIVDRPRLA 310 Lambda K H 0.317 0.138 0.412 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: 15 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: 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 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
Align candidate HSERO_RS06545 HSERO_RS06545 (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.31384.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-147 473.7 0.0 9.2e-147 473.5 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS06545 HSERO_RS06545 catechol 1,2-dioxy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS06545 HSERO_RS06545 catechol 1,2-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.5 0.0 9.2e-147 9.2e-147 2 285 .] 8 292 .. 7 292 .. 0.99 Alignments for each domain: == domain 1 score: 473.5 bits; conditional E-value: 9.2e-147 TIGR02439 2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelglla 69 t+evq++l+ ++gl++eggn+r+kqiv+r+lsdlfk+iedl+it+de+wa+v+y+n+lG+a+e+gll+ lcl|FitnessBrowser__HerbieS:HSERO_RS06545 8 TREVQDFLRLASGLDTEGGNPRTKQIVHRILSDLFKTIEDLEITSDEYWAGVAYINRLGTAHEAGLLS 75 789***************************************************************** PP TIGR02439 70 aGlGlehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvld 137 +GlGl++fld+r+da da+ g+ ggtPrtieGPlyvaGapv +Gfarlddgs d++++t++++G+v+ lcl|FitnessBrowser__HerbieS:HSERO_RS06545 76 PGLGLDRFLDMRMDAEDAALGIAGGTPRTIEGPLYVAGAPVEQGFARLDDGS-DKSGQTIIMHGTVYG 142 ****************************************************.666************ PP TIGR02439 138 aeGkpiagakvevwhanskGnysffdks..qsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqq 203 a+Gkp++ga+vevwhan+kG+ys+fd++ q +fn+rrtiitda+G+y++rs++P+ yg+pp+gptq lcl|FitnessBrowser__HerbieS:HSERO_RS06545 143 ADGKPMPGAQVEVWHANTKGFYSHFDPTgeQKPFNMRRTIITDAQGRYKFRSIMPTAYGCPPAGPTQG 210 ****************************99************************************** PP TIGR02439 204 llnllGrhGerPahvhffvsapgyrklttqinlegdkylyddfafatreglvaevkevedaaaakrrg 271 lln+lGrhG+rPah+hffv+a+g+rklttqin+egd+++yddfa+atreglv+ + e++daa++k++g lcl|FitnessBrowser__HerbieS:HSERO_RS06545 211 LLNALGRHGNRPAHIHFFVTAEGHRKLTTQINIEGDPLIYDDFAYATREGLVPPLVERTDAASIKAEG 278 ******************************************************************** PP TIGR02439 272 vegrfaeiefdlel 285 +eg+faei+fd++l lcl|FitnessBrowser__HerbieS:HSERO_RS06545 279 LEGPFAEIVFDIKL 292 ************97 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.61 // [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