Align catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate H281DRAFT_01074 H281DRAFT_01074 catechol 1,2-dioxygenase
Query= BRENDA::Q8GAY6 (311 letters) >FitnessBrowser__Burk376:H281DRAFT_01074 Length = 311 Score = 536 bits (1381), Expect = e-157 Identities = 258/308 (83%), Positives = 281/308 (91%) Query: 1 MSVKVFDTKEVQDLLKAAANMGSEDGSARAKQIVNRLLGDLFKAIDDLDMTPDEIWAGVH 60 M+ KVF T EVQ+LL AAAN+G EDG+ARAK+I +RLL DLFKAIDDLDMTPDEIWAGV Sbjct: 1 MNAKVFKTNEVQNLLAAAANLGREDGNARAKEITHRLLSDLFKAIDDLDMTPDEIWAGVT 60 Query: 61 YFNKLGQDGEAALLAAGLGLEKFLDIRMDAEDKAAEITGGTPRTIEGPLYVAGAPVRDGI 120 YFNKLGQDGEAALLAAGLGLEK+LDIRMDA+D A+I GGTPRTIEGPLYVAGAPVRDG+ Sbjct: 61 YFNKLGQDGEAALLAAGLGLEKYLDIRMDAQDLEADIHGGTPRTIEGPLYVAGAPVRDGV 120 Query: 121 SKIDVNPDEGAGPLVIRGTVTGPDGKPVANALVECWHANSKGFYSHFDPTGAQSEFNLRG 180 SKID+NPD AGPL+I GTVTGPD KPVA A+VECWHANSKGFYSHFDPTGAQSEFNLRG Sbjct: 121 SKIDINPDADAGPLIIHGTVTGPDRKPVAGAVVECWHANSKGFYSHFDPTGAQSEFNLRG 180 Query: 181 AVSTDVDGKYEFRTLMPVGYGCPPHGATQQLLNVLARHGNRPAHVHFFVTTDKYRKLTTQ 240 AV T DGKYEFRTLMPVGYGCPP GATQQLLN+LARHGNRPAHVHFFVT+DK RKLTTQ Sbjct: 181 AVRTGADGKYEFRTLMPVGYGCPPQGATQQLLNMLARHGNRPAHVHFFVTSDKTRKLTTQ 240 Query: 241 INIEGDPLIWDDFAYATREDLIPHVVEKTGGTPLGMKADTYKEIEFNIELTPLVHGKDNQ 300 INIEGDPLIWDDFAYATRE+L+PHVVEKTGG LG+KAD YKEI+F+I L+PL+ GKDNQ Sbjct: 241 INIEGDPLIWDDFAYATREELVPHVVEKTGGIALGLKADAYKEIQFDIALSPLIEGKDNQ 300 Query: 301 LVSRLRAS 308 LV+R RAS Sbjct: 301 LVNRPRAS 308 Lambda K H 0.317 0.137 0.409 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: 457 Number of extensions: 7 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 H281DRAFT_01074 H281DRAFT_01074 (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.21842.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-134 432.3 0.0 3.8e-134 432.1 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_01074 H281DRAFT_01074 catechol 1,2-dio Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_01074 H281DRAFT_01074 catechol 1,2-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 432.1 0.0 3.8e-134 3.8e-134 2 285 .] 8 290 .. 7 290 .. 0.98 Alignments for each domain: == domain 1 score: 432.1 bits; conditional E-value: 3.8e-134 TIGR02439 2 tkevqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgl 67 t+evq+ll ++a+l +e+gnar+k i +r+lsdlfkai+dld+t+de+wa+v y+nklGq++e++l lcl|FitnessBrowser__Burk376:H281DRAFT_01074 8 TNEVQNLLAAAANLGREDGNARAKEITHRLLSDLFKAIDDLDMTPDEIWAGVTYFNKLGQDGEAAL 73 789*************************************************************** PP TIGR02439 68 laaGlGlehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkG 133 laaGlGle++ld+r+da+d +a+++ggtPrtieGPlyvaGapv +G++++d +++ d a +l+++G lcl|FitnessBrowser__Burk376:H281DRAFT_01074 74 LAAGLGLEKYLDIRMDAQDLEADIHGGTPRTIEGPLYVAGAPVRDGVSKIDINPDAD-AGPLIIHG 138 ******************************************************655.99****** PP TIGR02439 134 qvldaeGkpiagakvevwhanskGnysffdks..qsefnlrrtiitdaeGkyrarsvvPvGygvpp 197 +v+ + kp+aga+ve+whanskG+ys+fd++ qsefnlr++++t+a+Gky++r+++PvGyg+pp lcl|FitnessBrowser__Burk376:H281DRAFT_01074 139 TVTGPDRKPVAGAVVECWHANSKGFYSHFDPTgaQSEFNLRGAVRTGADGKYEFRTLMPVGYGCPP 204 *******************************999******************************** PP TIGR02439 198 qgptqqllnllGrhGerPahvhffvsapgyrklttqinlegdkylyddfafatreglvaevkeved 263 qg+tqqlln+l rhG+rPahvhffv+++ rklttqin+egd++++ddfa+atre+lv++v e+++ lcl|FitnessBrowser__Burk376:H281DRAFT_01074 205 QGATQQLLNMLARHGNRPAHVHFFVTSDKTRKLTTQINIEGDPLIWDDFAYATREELVPHVVEKTG 270 ****************************************************************** PP TIGR02439 264 aaaakrrgvegrfaeiefdlel 285 a +++ ++ei+fd+ l lcl|FitnessBrowser__Burk376:H281DRAFT_01074 271 GIALG--LKADAYKEIQFDIAL 290 99998..8899********986 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.41 // [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