Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate HSERO_RS06525 HSERO_RS06525 3-oxoadipate enol-lactonase
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >FitnessBrowser__HerbieS:HSERO_RS06525 Length = 261 Score = 284 bits (726), Expect = 2e-81 Identities = 140/253 (55%), Positives = 181/253 (71%), Gaps = 3/253 (1%) Query: 11 LKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSLVTPGPYSI 70 L YQL+G PVLVLSNSLGT+L MWD Q+P + +HFRVLR+DTRGHG+S VTPG SI Sbjct: 11 LHYQLEGDASLPVLVLSNSLGTSLSMWDPQMPQWLQHFRVLRYDTRGHGQSEVTPGECSI 70 Query: 71 EQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAAKIGDPSVW 130 QLG DV+ALLD L I +AHFCGLSMGG WL ++ +R++KL++CNT AKIG W Sbjct: 71 AQLGSDVIALLDHLGIAQAHFCGLSMGGSTFMWLAVHHPQRINKLILCNTGAKIGTAEAW 130 Query: 131 NPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQGYAANCAA 190 N RIETV R+G + A+ A ++RW TP++AQA+P + +T ML AT +GYAA CAA Sbjct: 131 NSRIETVRREG---LGAIAGAVVSRWLTPEYAQAHPQQVQALTAMLLATPAEGYAAACAA 187 Query: 191 VRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYAAHLSNVQAGS 250 VRD D RE +A I PTL+IAG+ D TPP+ +F++ + GA+Y EF AAH+SN Q + Sbjct: 188 VRDHDLREAIAGIRAPTLIIAGSGDVPTPPADAQFMRATIPGAQYVEFDAAHISNQQQAA 247 Query: 251 AFSDRVLSFLLAE 263 AF+ V+ FL + Sbjct: 248 AFTQAVVQFLTGQ 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: 238 Number of extensions: 12 Number of successful extensions: 2 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: 261 Length adjustment: 25 Effective length of query: 241 Effective length of database: 236 Effective search space: 56876 Effective search space used: 56876 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 HSERO_RS06525 HSERO_RS06525 (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.8135.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-103 331.9 0.5 1.3e-103 331.8 0.5 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS06525 HSERO_RS06525 3-oxoadipate enol- Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS06525 HSERO_RS06525 3-oxoadipate enol-lactonase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 331.8 0.5 1.3e-103 1.3e-103 1 251 [] 10 258 .. 10 258 .. 0.99 Alignments for each domain: == domain 1 score: 331.8 bits; conditional E-value: 1.3e-103 TIGR02427 1 rlhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladd 68 rlhy+leg++ + pvlvl+nSLGt+l++wd+++++ ++frvlryD+rGHG+S+v+ g+ si++l++d lcl|FitnessBrowser__HerbieS:HSERO_RS06525 10 RLHYQLEGDA-SLPVLVLSNSLGTSLSMWDPQMPQWLQHFRVLRYDTRGHGQSEVTPGECSIAQLGSD 76 69********.********************************************************* PP TIGR02427 69 vlallDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaa 136 v+allD+lgi++a++cGlS+GG + ++La+++p+r+++l+l+nt akigtae W++Ri++vr+eGl a lcl|FitnessBrowser__HerbieS:HSERO_RS06525 77 VIALLDHLGIAQAHFCGLSMGGSTFMWLAVHHPQRINKLILCNTGAKIGTAEAWNSRIETVRREGLGA 144 ******************************************************************** PP TIGR02427 137 ladavlerwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeD 204 +a av++rw tp++++a+p++++++++ml+++p+egYaa+caA+rd dlre++ i++Ptl+iaG+ D lcl|FitnessBrowser__HerbieS:HSERO_RS06525 145 IAGAVVSRWLTPEYAQAHPQQVQALTAMLLATPAEGYAAACAAVRDHDLREAIAGIRAPTLIIAGSGD 212 ******************************************************************** PP TIGR02427 205 gstPpelvreiadlvpgarfaeieeaaHlpnleqpeafaallrdflk 251 + tPp++++ + +++pga+++e++ aaH++n +q++af++++++fl+ lcl|FitnessBrowser__HerbieS:HSERO_RS06525 213 VPTPPADAQFMRATIPGAQYVEFD-AAHISNQQQAAAFTQAVVQFLT 258 ************************.********************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (251 nodes) Target sequences: 1 (261 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: 6.84 // [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