Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate GFF446 PGA1_c04570 putative 3-oxoadipate enol-lactonase
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >FitnessBrowser__Phaeo:GFF446 Length = 262 Score = 186 bits (471), Expect = 6e-52 Identities = 105/265 (39%), Positives = 152/265 (57%), Gaps = 6/265 (2%) Query: 3 FVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSL 62 FV L D +L YQLDG P LV +NSLGT+LH+WD+ + K R++R+D RGHG + Sbjct: 3 FVDLGDVQLHYQLDGTADGPPLVFANSLGTDLHVWDLVVERLPKELRIIRYDLRGHGGTP 62 Query: 63 VTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAA 122 TP PYS+ L RD LLD L ++ F GLS+GG+I Q L I + + LV+ NTAA Sbjct: 63 ATPAPYSMGTLVRDAERLLDQLQVKGCIFVGLSIGGMIAQGLAIKRLDLMRGLVLSNTAA 122 Query: 123 KIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQ 182 KIG + W RIE + RDG + A+ D + RWF P F + +P ++ +L S + Sbjct: 123 KIGTAAAWQQRIEAIKRDG---IDAVADTIMERWFAPAF-RKSPELSHWRAHLL-QQSVE 177 Query: 183 GYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEF-YAA 241 GY CAA+ DF + + +PTL IAG++D TP R + + G+++ A Sbjct: 178 GYIGCCAAISGTDFYTPTSGLRLPTLGIAGSDDGATPADLVRETVDLIPGSKFELIRRAG 237 Query: 242 HLSNVQAGSAFSDRVLSFLLAEKSI 266 H+ V+ F+DR+++FL + I Sbjct: 238 HIPCVEQPEVFADRLITFLTEQGHI 262 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: 232 Number of extensions: 13 Number of successful extensions: 4 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 GFF446 PGA1_c04570 (putative 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.4372.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-99 315.8 0.0 1.1e-98 315.6 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF446 PGA1_c04570 putative 3-oxoadipat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF446 PGA1_c04570 putative 3-oxoadipate enol-lactonase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 315.6 0.0 1.1e-98 1.1e-98 1 251 [] 10 257 .. 10 257 .. 0.98 Alignments for each domain: == domain 1 score: 315.6 bits; conditional E-value: 1.1e-98 TIGR02427 1 rlhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdvlallDalg 77 +lhy+l+g++ d p lv+ nSLGtdl++wd v+e+l k++r++ryD rGHG ++ +pys+++l++d +llD+l+ lcl|FitnessBrowser__Phaeo:GFF446 10 QLHYQLDGTA-DGPPLVFANSLGTDLHVWDLVVERLPKELRIIRYDLRGHGGTPATPAPYSMGTLVRDAERLLDQLQ 85 59********.8999************************************************************** PP TIGR02427 78 iekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaaladavlerwFtpafreae 154 ++ ++GlS+GG+iaq+La++r d+++ lvlsntaakigta W++Ri+a++++G+ a+ad+++erwF+pafr + lcl|FitnessBrowser__Phaeo:GFF446 86 VKGCIFVGLSIGGMIAQGLAIKRLDLMRGLVLSNTAAKIGTAAAWQQRIEAIKRDGIDAVADTIMERWFAPAFR--K 160 **************************************************************************..5 PP TIGR02427 155 paelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgstPpelvreiadlvpgarfaeieeaa 231 el+++r+ l++q++egY+++caAi +d+++ ++ +++Ptl iaG++Dg+tP++lvre++dl+pg++f+ i+ a+ lcl|FitnessBrowser__Phaeo:GFF446 161 SPELSHWRAHLLQQSVEGYIGCCAAISGTDFYTPTSGLRLPTLGIAGSDDGATPADLVRETVDLIPGSKFELIRRAG 237 66778************************************************************************ PP TIGR02427 232 Hlpnleqpeafaallrdflk 251 H+p++eqpe fa++l++fl+ lcl|FitnessBrowser__Phaeo:GFF446 238 HIPCVEQPEVFADRLITFLT 257 ******************95 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: 10.90 // [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