Align catechol 1,2-dioxygenase 1; EC 1.13.11.1 (characterized)
to candidate H281DRAFT_01643 H281DRAFT_01643 catechol 1,2-dioxygenase
Query= CharProtDB::CH_014952 (311 letters) >FitnessBrowser__Burk376:H281DRAFT_01643 Length = 312 Score = 520 bits (1338), Expect = e-152 Identities = 253/311 (81%), Positives = 271/311 (87%) Query: 1 MSIKVFGTKEVQDLLKAATNLEGKGGNARSKQIVHRLLSDLFKAIDDLDITPDEVWAGVN 60 M++KVF T+EVQDLLKAA NL+ G+AR+KQI HRLLSDLFKAIDDLDITPDE WAGVN Sbjct: 2 MNVKVFATQEVQDLLKAAANLDSDKGDARTKQIAHRLLSDLFKAIDDLDITPDETWAGVN 61 Query: 61 YLNKLGQDGEATLLAAGSGLEKYLDIRLDAADKAEGIEGGTPRTIEGPLYVAGATVHDGV 120 YLNKLGQDGEA LLAAG GLEKYLDIR+DA D+ I+GGTPRTIEGPLYV GA V DGV Sbjct: 62 YLNKLGQDGEAALLAAGLGLEKYLDIRMDAEDRQAEIDGGTPRTIEGPLYVEGAPVRDGV 121 Query: 121 SKIDINPDEDAGPLVIHGTVTGPDGKPVAGAVVECWHANSKGFYSHFDPTGAQSDFNLRG 180 SKID++ D DAGPLVI GTV GPDGKPVAGAVVECWHANSKGFYSHFDPTGAQS FNLRG Sbjct: 122 SKIDLDADADAGPLVIRGTVRGPDGKPVAGAVVECWHANSKGFYSHFDPTGAQSPFNLRG 181 Query: 181 AVKTGADGKYEFRTLMPVGYGCPPQGATQQLLNVLGRHGNRPAHVHFFVSSDSARKLTTQ 240 AV+T DG YEFRTLMPVGYGCPPQGATQQLLNVL RHGNRPAHVHFFV +D RKLTTQ Sbjct: 182 AVRTQDDGTYEFRTLMPVGYGCPPQGATQQLLNVLARHGNRPAHVHFFVKADGLRKLTTQ 241 Query: 241 FNIEGDPLIWDDFAYATREELIPPVTEKKGGTALGLKADTYKDIEFNLTLTSLVKGKDNQ 300 NIEGDPLIWDDFAYATRE+LIPPV K GG ALGLK D YK+IEFN TLT LV+GKDNQ Sbjct: 242 INIEGDPLIWDDFAYATREDLIPPVVGKSGGAALGLKDDAYKEIEFNFTLTPLVEGKDNQ 301 Query: 301 VVHRLRAEVAA 311 +V+RLR AA Sbjct: 302 LVNRLRTAAAA 312 Lambda K H 0.316 0.136 0.404 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: 479 Number of extensions: 16 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: 312 Length adjustment: 27 Effective length of query: 284 Effective length of database: 285 Effective search space: 80940 Effective search space used: 80940 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: 42 (22.0 bits) S2: 48 (23.1 bits)
Align candidate H281DRAFT_01643 H281DRAFT_01643 (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.8427.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-138 444.6 0.0 6.7e-138 444.4 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_01643 H281DRAFT_01643 catechol 1,2-dio Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_01643 H281DRAFT_01643 catechol 1,2-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 444.4 0.0 6.7e-138 6.7e-138 2 285 .] 9 291 .. 8 291 .. 0.99 Alignments for each domain: == domain 1 score: 444.4 bits; conditional E-value: 6.7e-138 TIGR02439 2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgl 67 t+evq+llk++a+l++++g+ar+kqi +r+lsdlfkai+dldit+de wa+v+ylnklGq++e++l lcl|FitnessBrowser__Burk376:H281DRAFT_01643 9 TQEVQDLLKAAANLDSDKGDARTKQIAHRLLSDLFKAIDDLDITPDETWAGVNYLNKLGQDGEAAL 74 79**************************************************************** PP TIGR02439 68 laaGlGlehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkG 133 laaGlGle++ld+r+da d++a+++ggtPrtieGPlyv Gapv +G++++d +++ d a +lv++G lcl|FitnessBrowser__Burk376:H281DRAFT_01643 75 LAAGLGLEKYLDIRMDAEDRQAEIDGGTPRTIEGPLYVEGAPVRDGVSKIDLDADAD-AGPLVIRG 139 ******************************************************555.99****** PP TIGR02439 134 qvldaeGkpiagakvevwhanskGnysffdks..qsefnlrrtiitdaeGkyrarsvvPvGygvpp 197 +v+ +Gkp+aga+ve+whanskG+ys+fd++ qs+fnlr++++t+++G+y++r+++PvGyg+pp lcl|FitnessBrowser__Burk376:H281DRAFT_01643 140 TVRGPDGKPVAGAVVECWHANSKGFYSHFDPTgaQSPFNLRGAVRTQDDGTYEFRTLMPVGYGCPP 205 *******************************999******************************** PP TIGR02439 198 qgptqqllnllGrhGerPahvhffvsapgyrklttqinlegdkylyddfafatreglvaevkeved 263 qg+tqqlln+l rhG+rPahvhffv a+g rklttqin+egd++++ddfa+atre+l++ v +++ lcl|FitnessBrowser__Burk376:H281DRAFT_01643 206 QGATQQLLNVLARHGNRPAHVHFFVKADGLRKLTTQINIEGDPLIWDDFAYATREDLIPPVVGKSG 271 ****************************************************************** PP TIGR02439 264 aaaakrrgvegrfaeiefdlel 285 aa +++ ++eief+++l lcl|FitnessBrowser__Burk376:H281DRAFT_01643 272 GAALG--LKDDAYKEIEFNFTL 291 *9999..899**********87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (312 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: 00:00:00.00 # Mc/sec: 9.32 // [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