Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate GFF3011 Psest_3069 3-oxoadipate enol-lactonase
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >FitnessBrowser__psRCH2:GFF3011 Length = 262 Score = 358 bits (919), Expect = e-104 Identities = 179/257 (69%), Positives = 205/257 (79%) Query: 4 VQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSLV 63 V+LAD L Y+ DG E+APVLVLSNSLGT+L MWD QI AF +HFRVLR+DTRGHG S V Sbjct: 4 VKLADVSLNYRFDGAENAPVLVLSNSLGTDLQMWDDQIAAFAEHFRVLRYDTRGHGGSGV 63 Query: 64 TPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAAK 123 TPGPYSIEQLG+DVL +LDA IER FCGLSMGGLIGQWLGI+AGERL +LV+CNT AK Sbjct: 64 TPGPYSIEQLGQDVLGMLDAFGIERFAFCGLSMGGLIGQWLGIHAGERLQRLVLCNTGAK 123 Query: 124 IGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQG 183 IG VWN RI++VL M +RDASIARWFT DFAQANPAVA +ITDM+A+TSP G Sbjct: 124 IGTDEVWNTRIDSVLAGREQTMRDMRDASIARWFTADFAQANPAVAARITDMIASTSPDG 183 Query: 184 YAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYAAHL 243 YAANCAAVRDAD+REQLA+I PTL++ G +D VT G FIQ + GAE F AAHL Sbjct: 184 YAANCAAVRDADYREQLATIKTPTLIVCGAKDPVTTVEHGEFIQANIPGAELVAFEAAHL 243 Query: 244 SNVQAGSAFSDRVLSFL 260 SNV+AG AF+ RVL+FL Sbjct: 244 SNVEAGDAFTQRVLTFL 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: 292 Number of extensions: 9 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 GFF3011 Psest_3069 (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.19578.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-102 326.4 0.1 6.4e-102 326.2 0.1 1.0 1 lcl|FitnessBrowser__psRCH2:GFF3011 Psest_3069 3-oxoadipate enol-lac Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF3011 Psest_3069 3-oxoadipate enol-lactonase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 326.2 0.1 6.4e-102 6.4e-102 2 251 .] 11 261 .. 10 261 .. 0.98 Alignments for each domain: == domain 1 score: 326.2 bits; conditional E-value: 6.4e-102 TIGR02427 2 lhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlallDal 76 l+yr++gae ++pvlvl+nSLGtdl++wd++++a++++frvlryD+rGHG S v+ gpysie+l++dvl++lDa+ lcl|FitnessBrowser__psRCH2:GFF3011 11 LNYRFDGAE-NAPVLVLSNSLGTDLQMWDDQIAAFAEHFRVLRYDTRGHGGSGVTPGPYSIEQLGQDVLGMLDAF 84 89*******.***************************************************************** PP TIGR02427 77 giekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaav...raeGlaaladavlerwFtp 148 gie++a+cGlS+GGli+q+L++++++r+++lvl+nt akigt e+W++Ri+ v r++ + ++da+++rwFt+ lcl|FitnessBrowser__psRCH2:GFF3011 85 GIERFAFCGLSMGGLIGQWLGIHAGERLQRLVLCNTGAKIGTDEVWNTRIDSVlagREQTMRDMRDASIARWFTA 159 ***************************************************994445677*************** PP TIGR02427 149 afreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadlvpgar 223 +f++a+pa ++ +++m+++++p+gYaa+caA+rdad+re+l i+ Ptl++ G++D++t e+ + i++ +pga+ lcl|FitnessBrowser__psRCH2:GFF3011 160 DFAQANPAVAARITDMIASTSPDGYAANCAAVRDADYREQLATIKTPTLIVCGAKDPVTTVEHGEFIQANIPGAE 234 *************************************************************************** PP TIGR02427 224 faeieeaaHlpnleqpeafaallrdflk 251 ++ +e aaHl+n+e+++af++++ +fl+ lcl|FitnessBrowser__psRCH2:GFF3011 235 LVAFE-AAHLSNVEAGDAFTQRVLTFLR 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.22 // [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