Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate WP_090446759.1 BLS63_RS16755 3-oxoadipate enol-lactonase
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >NCBI__GCF_900100495.1:WP_090446759.1 Length = 262 Score = 360 bits (924), Expect = e-104 Identities = 176/257 (68%), Positives = 208/257 (80%) Query: 4 VQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSLV 63 V LADG+L YQL+GP APVL+LSNSLGT+LHMWD QIPAFT+HF+VLR+DTRGHG+S+V Sbjct: 4 VHLADGDLNYQLEGPAGAPVLLLSNSLGTDLHMWDAQIPAFTQHFQVLRYDTRGHGQSVV 63 Query: 64 TPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAAK 123 + GPYSIEQLGRDVLALLDAL+I +A FCGLSMGGLIGQWL INA +R+ +LV+CNTAAK Sbjct: 64 SEGPYSIEQLGRDVLALLDALDIAKASFCGLSMGGLIGQWLAINAPQRIERLVLCNTAAK 123 Query: 124 IGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQG 183 IG P VWNPRI++VL G AM LRDASIARWFT FA A P + + MLA TSP G Sbjct: 124 IGSPEVWNPRIDSVLAGGTQAMRELRDASIARWFTAAFAAAQPEKVEPVVGMLAQTSPDG 183 Query: 184 YAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYAAHL 243 YAANCAAVRDADFREQ+A+I TL++ G+ D VT + GRF+ ER+ GA+ E +AAHL Sbjct: 184 YAANCAAVRDADFREQIAAIAASTLIVCGSADPVTTVADGRFMAERIVGAQLLELHAAHL 243 Query: 244 SNVQAGSAFSDRVLSFL 260 SNV+AG AF+ VL FL Sbjct: 244 SNVEAGVAFTQAVLEFL 260 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: 287 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: 262 Length adjustment: 25 Effective length of query: 241 Effective length of database: 237 Effective search space: 57117 Effective search space used: 57117 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 WP_090446759.1 BLS63_RS16755 (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.24755.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-102 326.2 0.3 7.3e-102 326.0 0.3 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090446759.1 BLS63_RS16755 3-oxoadipate enol- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090446759.1 BLS63_RS16755 3-oxoadipate enol-lactonase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 326.0 0.3 7.3e-102 7.3e-102 2 251 .] 11 261 .. 10 261 .. 0.98 Alignments for each domain: == domain 1 score: 326.0 bits; conditional E-value: 7.3e-102 TIGR02427 2 lhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvl 70 l+y+leg++ ++pvl+l+nSLGtdl++wd++++a+t++f+vlryD+rGHG+S v egpysie+l++dvl lcl|NCBI__GCF_900100495.1:WP_090446759.1 11 LNYQLEGPA-GAPVLLLSNSLGTDLHMWDAQIPAFTQHFQVLRYDTRGHGQSVVSEGPYSIEQLGRDVL 78 89*******.*********************************************************** PP TIGR02427 71 allDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeG...laa 136 allDal+i+ka +cGlS+GGli+q+La+++p+r+e+lvl+ntaakig++e+W++Ri+ v a G + lcl|NCBI__GCF_900100495.1:WP_090446759.1 79 ALLDALDIAKASFCGLSMGGLIGQWLAINAPQRIERLVLCNTAAKIGSPEVWNPRIDSVLAGGtqaMRE 147 ***************************************************************666667 PP TIGR02427 137 ladavlerwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDg 205 l+da+++rwFt+af++a+p+++e v ml++++p+gYaa+caA+rdad+re++ +ia+ tl++ G+ D+ lcl|NCBI__GCF_900100495.1:WP_090446759.1 148 LRDASIARWFTAAFAAAQPEKVEPVVGMLAQTSPDGYAANCAAVRDADFREQIAAIAASTLIVCGSADP 216 89******************************************************************* PP TIGR02427 206 stPpelvreiadlvpgarfaeieeaaHlpnleqpeafaallrdflk 251 +t ++ r +a+ + ga++ e++ aaHl+n+e++ af++++ +fl+ lcl|NCBI__GCF_900100495.1:WP_090446759.1 217 VTTVADGRFMAERIVGAQLLELH-AAHLSNVEAGVAFTQAVLEFLQ 261 ***********************.********************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (251 nodes) Target sequences: 1 (262 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: 9.22 // [ok]
This GapMind analysis is from Sep 24 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