Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate RR42_RS10690 RR42_RS10690 3-oxoadipate enol-lactonase
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >FitnessBrowser__Cup4G11:RR42_RS10690 Length = 259 Score = 288 bits (738), Expect = 6e-83 Identities = 143/258 (55%), Positives = 181/258 (70%), Gaps = 3/258 (1%) Query: 3 FVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSL 62 F + L Y+LDG + PVLVL+NSLGTNL MW+ QI AF KHFRVLR+DTRGHG+S Sbjct: 3 FAEFPGVRLHYRLDGDDTLPVLVLANSLGTNLDMWNPQIEAFAKHFRVLRYDTRGHGQSS 62 Query: 63 VTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAA 122 VTPGPY+I QLG DV+ALLDAL I+RAHFCGLSMGG+ G WL +N R K+V+CNTAA Sbjct: 63 VTPGPYTIPQLGEDVIALLDALKIDRAHFCGLSMGGITGMWLALNHAGRFDKVVLCNTAA 122 Query: 123 KIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQ 182 IG W R V RDG + ++ +A + +W TP +A PA+ + + ML+AT Sbjct: 123 YIGPAENWTNRAAAVERDG---VGSIANAVVDKWLTPGYAAGQPALVQLLQAMLSATDAA 179 Query: 183 GYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYAAH 242 GYAANC AVRD+D R+ +A IT PTLVIAG+ D TPP G+++ +++ GA YAE AAH Sbjct: 180 GYAANCRAVRDSDLRDAVAGITRPTLVIAGSGDIPTPPHDGQYLAQKIPGARYAELDAAH 239 Query: 243 LSNVQAGSAFSDRVLSFL 260 LSN++ F+D VL FL Sbjct: 240 LSNLEQVEGFTDAVLEFL 257 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: 272 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: 259 Length adjustment: 25 Effective length of query: 241 Effective length of database: 234 Effective search space: 56394 Effective search space used: 56394 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 RR42_RS10690 RR42_RS10690 (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.21672.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-99 318.4 0.0 1.8e-99 318.2 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS10690 RR42_RS10690 3-oxoadipate enol-l Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS10690 RR42_RS10690 3-oxoadipate enol-lactonase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 318.2 0.0 1.8e-99 1.8e-99 1 251 [] 10 258 .. 10 258 .. 0.99 Alignments for each domain: == domain 1 score: 318.2 bits; conditional E-value: 1.8e-99 TIGR02427 1 rlhyrlegaeadkpvlvlinSLGtdlrlwdkvlealtkdfrvlryDkrGHGlSdvpegpysiedladdv 69 rlhyrl+g++ pvlvl nSLGt+l +w++++ea++k+frvlryD+rGHG+S+v+ gpy+i +l++dv lcl|FitnessBrowser__Cup4G11:RR42_RS10690 10 RLHYRLDGDD-TLPVLVLANSLGTNLDMWNPQIEAFAKHFRVLRYDTRGHGQSSVTPGPYTIPQLGEDV 77 69*******9.9********************************************************* PP TIGR02427 70 lallDalgiekaavcGlSlGGliaqaLaarrpdrvealvlsntaakigtaesWeaRiaavraeGlaala 138 +allDal+i++a++cGlS+GG+++++La++++ r++++vl+ntaa ig ae W +R+aav+++G+ ++a lcl|FitnessBrowser__Cup4G11:RR42_RS10690 78 IALLDALKIDRAHFCGLSMGGITGMWLALNHAGRFDKVVLCNTAAYIGPAENWTNRAAAVERDGVGSIA 146 ********************************************************************* PP TIGR02427 139 davlerwFtpafreaepaelelvrnmlveqppegYaatcaAirdadlrerleeiavPtlviaGdeDgst 207 +av+++w tp++++ +pa ++l+++ml +++++gYaa+c A+rd dlr+++ i+ PtlviaG+ D+ t lcl|FitnessBrowser__Cup4G11:RR42_RS10690 147 NAVVDKWLTPGYAAGQPALVQLLQAMLSATDAAGYAANCRAVRDSDLRDAVAGITRPTLVIAGSGDIPT 215 ********************************************************************* PP TIGR02427 208 PpelvreiadlvpgarfaeieeaaHlpnleqpeafaallrdflk 251 Pp++ + +a+++pgar+ae++ aaHl+nleq e f++++ +fl+ lcl|FitnessBrowser__Cup4G11:RR42_RS10690 216 PPHDGQYLAQKIPGARYAELD-AAHLSNLEQVEGFTDAVLEFLQ 258 *********************.********************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (251 nodes) Target sequences: 1 (259 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: 9.38 // [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