Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate Pf6N2E2_2830 Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24)
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2830 Length = 266 Score = 462 bits (1190), Expect = e-135 Identities = 227/261 (86%), Positives = 245/261 (93%) Query: 1 VGFVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGR 60 VGFV+LA+G+L Y+ DGP+ APVLVLSNSLGT+LHMWD Q+ AF++HFRVLRFDTRGHG+ Sbjct: 1 VGFVKLAEGDLNYRFDGPQDAPVLVLSNSLGTDLHMWDEQVAAFSEHFRVLRFDTRGHGQ 60 Query: 61 SLVTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNT 120 SLVT GPYSIEQLGRDVLA+LD LNI++ HFCGLSMGGLIGQWLGINAGERL+KLVVCNT Sbjct: 61 SLVTEGPYSIEQLGRDVLAMLDQLNIDKVHFCGLSMGGLIGQWLGINAGERLYKLVVCNT 120 Query: 121 AAKIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATS 180 AAKIGDPSVWNPRIETVLRDG AAMVALRDASIARWFTPDFA+A PA AK+ITDMLAATS Sbjct: 121 AAKIGDPSVWNPRIETVLRDGKAAMVALRDASIARWFTPDFAEAQPATAKKITDMLAATS 180 Query: 181 PQGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYA 240 PQGYAANCAAVRDADFREQL+SI VP LVIAGTEDAVTPPSGG FIQERVRGAEYAEFYA Sbjct: 181 PQGYAANCAAVRDADFREQLSSIRVPLLVIAGTEDAVTPPSGGHFIQERVRGAEYAEFYA 240 Query: 241 AHLSNVQAGSAFSDRVLSFLL 261 AHLSNVQAG+AFS RVL FLL Sbjct: 241 AHLSNVQAGAAFSARVLDFLL 261 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: 351 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: 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 Pf6N2E2_2830 (Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24))
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.24445.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-108 347.3 0.0 2.7e-108 347.1 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2830 Beta-ketoadipate enol-lactone hy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2830 Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 347.1 0.0 2.7e-108 2.7e-108 2 250 .. 11 260 .. 10 261 .. 0.99 Alignments for each domain: == domain 1 score: 347.1 bits; conditional E-value: 2.7e-108 TIGR02427 2 lhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedl 65 l+yr++g++ d+pvlvl+nSLGtdl++wd++++a++++frvlr+D+rGHG+S v+egpysie+l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2830 11 LNYRFDGPQ-DAPVLVLSNSLGTDLHMWDEQVAAFSEHFRVLRFDTRGHGQSLVTEGPYSIEQL 73 89*******.****************************************************** PP TIGR02427 66 addvlallDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaav 129 ++dvla+lD+l+i+k+++cGlS+GGli+q+L++++++r+ +lv++ntaakig++++W++Ri++v lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2830 74 GRDVLAMLDQLNIDKVHFCGLSMGGLIGQWLGINAGERLYKLVVCNTAAKIGDPSVWNPRIETV 137 **************************************************************** PP TIGR02427 130 raeG...laaladavlerwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlrerle 190 ++G + al+da+++rwFtp+f+ea+pa+++++++ml++++p+gYaa+caA+rdad+re+l+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2830 138 LRDGkaaMVALRDASIARWFTPDFAEAQPATAKKITDMLAATSPQGYAANCAAVRDADFREQLS 201 ****999999****************************************************** PP TIGR02427 191 eiavPtlviaGdeDgstPpelvreiadlvpgarfaeieeaaHlpnleqpeafaallrdfl 250 +i+vP+lviaG+eD++tPp+ + i++ v ga++ae++ aaHl+n+++++af+a++ dfl lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2830 202 SIRVPLLVIAGTEDAVTPPSGGHFIQERVRGAEYAEFY-AAHLSNVQAGAAFSARVLDFL 260 **************************************.********************8 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.27 // [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