Align Catechol 1,2-dioxygenase (EC 1.13.11.1) (characterized)
to candidate BWI76_RS13700 BWI76_RS13700 catechol 1,2-dioxygenase
Query= reanno::pseudo3_N2E3:AO353_23525 (309 letters) >FitnessBrowser__Koxy:BWI76_RS13700 Length = 308 Score = 366 bits (940), Expect = e-106 Identities = 176/299 (58%), Positives = 223/299 (74%) Query: 10 SAQKFLEEASGLLNDAGNPRAKALIYRILRDSVNIIEDLEVTPEEFWKAVNYLNELGARQ 69 + Q L E++GL G+ R K +I+R+L + +I+D +T EEFW AVNYL+ELG RQ Sbjct: 10 AVQNLLRESAGLNISGGDERFKTIIHRLLENICTLIDDYNITEEEFWHAVNYLHELGGRQ 69 Query: 70 EAGLLVAGLGLEHYLDLLMDAEDAQAGKTGGTPRTIEGPLYVAGAPLSNGEARLDDGVDP 129 EA LL AGLGLEH+LDL DA DA + GTPRTIEGPLYVA APL++G R+DDG D Sbjct: 70 EAALLAAGLGLEHFLDLRQDAIDAAEQRETGTPRTIEGPLYVANAPLADGHTRMDDGKDA 129 Query: 130 GVVLFMQGQVKNTDGKPLAGAVVDVWHANTGGTYSYFDGSQSEFNLRRRIVTDAEGRYRF 189 G V+++ GQV +T G+P+A A+VD+WHANT G YS+FD SQSE+NLRRRI T A+GRY Sbjct: 130 GEVMWLYGQVNDTQGRPVANAIVDIWHANTLGNYSFFDKSQSEYNLRRRIRTGADGRYSV 189 Query: 190 RSIVPSGYGCPPDGPTQQLLDQLGRHGQRPAHIHFFISADDHRHLTTQINLDGDKYLHDD 249 RSI+PSGYGCPPDGPTQ+LL+QLGRHG RPAHIHFF+SA ++HLT+QINL+GDKYL DD Sbjct: 190 RSIMPSGYGCPPDGPTQKLLNQLGRHGNRPAHIHFFVSAPGYKHLTSQINLNGDKYLWDD 249 Query: 250 FAYATRDELIAKITFSDDQQRAREHGVSGRFAEIEFDFTLQSSAQPEEQHRHERVRALE 308 FA+ATRD LIA D++ ++ + G E+ FDFTL + +E+ R R+RA E Sbjct: 250 FAFATRDGLIADPVKVSDRELIQQRELDGEHTEVRFDFTLCKALNADEEQRGTRLRAQE 308 Lambda K H 0.317 0.136 0.401 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: 345 Number of extensions: 6 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: 309 Length of database: 308 Length adjustment: 27 Effective length of query: 282 Effective length of database: 281 Effective search space: 79242 Effective search space used: 79242 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 BWI76_RS13700 BWI76_RS13700 (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.3175.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-139 450.2 0.1 1.3e-139 450.0 0.1 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS13700 BWI76_RS13700 catechol 1,2-dioxy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS13700 BWI76_RS13700 catechol 1,2-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 450.0 0.1 1.3e-139 1.3e-139 4 285 .] 10 289 .. 7 289 .. 0.99 Alignments for each domain: == domain 1 score: 450.0 bits; conditional E-value: 1.3e-139 TIGR02439 4 evqallkkvagleqeggnarikqivlrvlsdlfkaiedlditedefwaaveylnklGqanelgllaaGlGl 74 vq+ll++ agl+ +gg++r+k i++r+l+++ +i+d++ite+efw+av+yl +lG ++e++llaaGlGl lcl|FitnessBrowser__Koxy:BWI76_RS13700 10 AVQNLLRESAGLNISGGDERFKTIIHRLLENICTLIDDYNITEEEFWHAVNYLHELGGRQEAALLAAGLGL 80 69********************************************************************* PP TIGR02439 75 ehfldlrldaadakagleggtPrtieGPlyvaGapvseGfarlddgseddkaetlvlkGqvldaeGkpiag 145 ehfldlr+da+da++++e gtPrtieGPlyva ap+++G++r+ddg+ d +e+++l Gqv d++G+p+a+ lcl|FitnessBrowser__Koxy:BWI76_RS13700 81 EHFLDLRQDAIDAAEQRETGTPRTIEGPLYVANAPLADGHTRMDDGK--DAGEVMWLYGQVNDTQGRPVAN 149 **********************************************9..668******************* PP TIGR02439 146 akvevwhanskGnysffdksqsefnlrrtiitdaeGkyrarsvvPvGygvppqgptqqllnllGrhGerPa 216 a+v++whan+ Gnysffdksqse+nlrr+i+t+a+G+y++rs++P+Gyg+pp+gptq+lln+lGrhG+rPa lcl|FitnessBrowser__Koxy:BWI76_RS13700 150 AIVDIWHANTLGNYSFFDKSQSEYNLRRRIRTGADGRYSVRSIMPSGYGCPPDGPTQKLLNQLGRHGNRPA 220 *********************************************************************** PP TIGR02439 217 hvhffvsapgyrklttqinlegdkylyddfafatreglvaevkevedaaaakrrgvegrfaeiefdlel 285 h+hffvsapgy++lt+qinl+gdkyl+ddfafatr+gl+a+ +v+d + +++r+++g+++e+ fd++l lcl|FitnessBrowser__Koxy:BWI76_RS13700 221 HIHFFVSAPGYKHLTSQINLNGDKYLWDDFAFATRDGLIADPVKVSDRELIQQRELDGEHTEVRFDFTL 289 *******************************************************************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (285 nodes) Target sequences: 1 (308 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: 00:00:00.00 # Mc/sec: 11.53 // [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