Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate AO353_17230 AO353_17230 3-oxoadipate enol-lactonase
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17230 Length = 266 Score = 532 bits (1371), Expect = e-156 Identities = 266/266 (100%), Positives = 266/266 (100%) Query: 1 VGFVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGR 60 VGFVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGR Sbjct: 1 VGFVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGR 60 Query: 61 SLVTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNT 120 SLVTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNT Sbjct: 61 SLVTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNT 120 Query: 121 AAKIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATS 180 AAKIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATS Sbjct: 121 AAKIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATS 180 Query: 181 PQGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYA 240 PQGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYA Sbjct: 181 PQGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYA 240 Query: 241 AHLSNVQAGSAFSDRVLSFLLAEKSI 266 AHLSNVQAGSAFSDRVLSFLLAEKSI Sbjct: 241 AHLSNVQAGSAFSDRVLSFLLAEKSI 266 Lambda K H 0.321 0.136 0.410 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: 412 Number of extensions: 5 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: 266 Length of database: 266 Length adjustment: 25 Effective length of query: 241 Effective length of database: 241 Effective search space: 58081 Effective search space used: 58081 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: 47 (22.7 bits)
Align candidate AO353_17230 AO353_17230 (3-oxoadipate enol-lactonase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))
# 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/TIGR02427.hmm # target sequence database: /tmp/gapView.8195.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02427 [M=251] Accession: TIGR02427 Description: protocat_pcaD: 3-oxoadipate enol-lactonase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-108 346.7 0.0 4.2e-108 346.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_17230 AO353_17230 3-oxoadipate enol-la Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_17230 AO353_17230 3-oxoadipate enol-lactonase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 346.5 0.0 4.2e-108 4.2e-108 2 250 .. 11 260 .. 10 261 .. 0.99 Alignments for each domain: == domain 1 score: 346.5 bits; conditional E-value: 4.2e-108 TIGR02427 2 lhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedla 66 l+y+l+g+e ++pvlvl+nSLGt+l++wd +++a+tk+frvlr+D+rGHG+S v+ gpysie+l+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_17230 11 LKYQLDGPE-HAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSLVTPGPYSIEQLG 74 89*******.******************************************************* PP TIGR02427 67 ddvlallDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavra 131 +dvlallDal+ie+a++cGlS+GGli+q+L++++++r+++lv++ntaakig++++W++Ri++v + lcl|FitnessBrowser__pseudo3_N2E3:AO353_17230 75 RDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAAKIGDPSVWNPRIETVLR 139 ***************************************************************** PP TIGR02427 132 eG...laaladavlerwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeia 193 +G + al+da+++rwFtp+f++a+pa ++++++ml++++p+gYaa+caA+rdad+re+l +i+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_17230 140 DGpaaMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQGYAANCAAVRDADFREQLASIT 204 **99999********************************************************** PP TIGR02427 194 vPtlviaGdeDgstPpelvreiadlvpgarfaeieeaaHlpnleqpeafaallrdfl 250 vPtlviaG+eD++tPp+ r i++ v ga++ae++ aaHl+n++++ af++++ +fl lcl|FitnessBrowser__pseudo3_N2E3:AO353_17230 205 VPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFY-AAHLSNVQAGSAFSDRVLSFL 260 ***********************************.*******************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (251 nodes) Target sequences: 1 (266 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: 6.13 // [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