Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate BWI76_RS16125 BWI76_RS16125 3-oxoadipate enol-lactonase
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >FitnessBrowser__Koxy:BWI76_RS16125 Length = 255 Score = 224 bits (570), Expect = 2e-63 Identities = 118/252 (46%), Positives = 156/252 (61%), Gaps = 4/252 (1%) Query: 13 YQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSLVTPGPYSIEQ 72 YQ+DGP+ APV+VLSNSLGT MW Q+ A T+HFRVLR+DT GHG + G ++ Q Sbjct: 5 YQIDGPQDAPVIVLSNSLGTTRAMWQPQLEALTQHFRVLRYDTHGHGATRKN-GKVTLAQ 63 Query: 73 LGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAAKIGDPSVWNP 132 LG DV+ALLD LNI +A FCG+SMGGL G WLG A ER + LVV NTAA+IGD + W Sbjct: 64 LGEDVVALLDHLNIAKAWFCGISMGGLTGLWLGRFAPERFYGLVVANTAARIGDQASWLS 123 Query: 133 RIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQGYAANCAAVR 192 R V ++G + A + RWFT F Q P V + L +GYAA C A+ Sbjct: 124 RARAVRQEGMDVVAA---GAADRWFTHAFRQKTPEVVAALCHQLTHIDAEGYAACCEALA 180 Query: 193 DADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYAAHLSNVQAGSAF 252 AD R ++A I +P L++AG D VT + F+ +++ +E A+HLSN++A AF Sbjct: 181 AADLRAEVAQIPIPVLIVAGESDPVTTVADADFLHQQIPVSEVVVLAASHLSNIEAPKAF 240 Query: 253 SDRVLSFLLAEK 264 S +L F+ EK Sbjct: 241 SSALLGFVQGEK 252 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: 197 Number of extensions: 6 Number of successful extensions: 3 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: 255 Length adjustment: 24 Effective length of query: 242 Effective length of database: 231 Effective search space: 55902 Effective search space used: 55902 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 BWI76_RS16125 BWI76_RS16125 (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.26354.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-88 280.0 1.3 8.9e-88 279.9 1.3 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS16125 BWI76_RS16125 3-oxoadipate enol- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS16125 BWI76_RS16125 3-oxoadipate enol-lactonase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 279.9 1.3 8.9e-88 8.9e-88 2 251 .] 3 249 .. 2 249 .. 0.98 Alignments for each domain: == domain 1 score: 279.9 bits; conditional E-value: 8.9e-88 TIGR02427 2 lhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlal 72 + y+++g++ d+pv+vl+nSLGt+ ++w+++lealt++frvlryD+ GHG+ +g++++++l++dv+al lcl|FitnessBrowser__Koxy:BWI76_RS16125 3 VDYQIDGPQ-DAPVIVLSNSLGTTRAMWQPQLEALTQHFRVLRYDTHGHGATR-KNGKVTLAQLGEDVVAL 71 679******.****************************************976.68899************ PP TIGR02427 73 lDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaaladavle 143 lD+l+i+ka +cG+S+GGl++++L+ +p+r+ lv++ntaa+ig++ sW +R++avr+eG+ ++a ++ + lcl|FitnessBrowser__Koxy:BWI76_RS16125 72 LDHLNIAKAWFCGISMGGLTGLWLGRFAPERFYGLVVANTAARIGDQASWLSRARAVRQEGMDVVAAGAAD 142 *********************************************************************** PP TIGR02427 144 rwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvre 214 rwFt+afr++ p+ ++++++ l++ ++egYaa+c+A+++adlr+++ +i +P+l++aG+ D++t ++++ lcl|FitnessBrowser__Koxy:BWI76_RS16125 143 RWFTHAFRQKTPEVVAALCHQLTHIDAEGYAACCEALAAADLRAEVAQIPIPVLIVAGESDPVTTVADADF 213 *********************************************************************** PP TIGR02427 215 iadlvpgarfaeieeaaHlpnleqpeafaallrdflk 251 + +++p +++++++ a+Hl+n+e+p+af+++l +f++ lcl|FitnessBrowser__Koxy:BWI76_RS16125 214 LHQQIPVSEVVVLA-ASHLSNIEAPKAFSSALLGFVQ 249 *************9.******************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (251 nodes) Target sequences: 1 (255 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: 00:00:00.00 # Mc/sec: 7.65 // [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