Align Imidazolonepropionase (EC 3.5.2.7) (characterized)
to candidate Pf6N2E2_3798 Imidazolonepropionase (EC 3.5.2.7)
Query= reanno::pseudo6_N2E2:Pf6N2E2_3798 (400 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3798 Length = 400 Score = 795 bits (2052), Expect = 0.0 Identities = 400/400 (100%), Positives = 400/400 (100%) Query: 1 MKTLWQNCHAATMAQGVYSIIEDAAIVTQGKHIQWIGPRAELPTGDYPAVNDLKGAWVTP 60 MKTLWQNCHAATMAQGVYSIIEDAAIVTQGKHIQWIGPRAELPTGDYPAVNDLKGAWVTP Sbjct: 1 MKTLWQNCHAATMAQGVYSIIEDAAIVTQGKHIQWIGPRAELPTGDYPAVNDLKGAWVTP 60 Query: 61 GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKR 120 GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKR Sbjct: 61 GLIDCHTHTVFGGNRSGEFEQRLQGVSYAEIAAAGGGIASTVRATRAASEDELFASAAKR 120 Query: 121 LGSLMRDGVTTVEIKSGYGLDLASERKILRVIRRLGAELPVSVRSTCLAAHALPPEYKDR 180 LGSLMRDGVTTVEIKSGYGLDLASERKILRVIRRLGAELPVSVRSTCLAAHALPPEYKDR Sbjct: 121 LGSLMRDGVTTVEIKSGYGLDLASERKILRVIRRLGAELPVSVRSTCLAAHALPPEYKDR 180 Query: 181 ADDYIEHICSEMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQQLGLPVKLHAEQL 240 ADDYIEHICSEMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQQLGLPVKLHAEQL Sbjct: 181 ADDYIEHICSEMLPALAAEGLVDAVDAFCEYLAFSPAQVERVFITAQQLGLPVKLHAEQL 240 Query: 241 SSLHGSSLAARYQALSADHLEFMTEDDAKAMAASGTVAVLLPGAFYFLRETQLPPMEALR 300 SSLHGSSLAARYQALSADHLEFMTEDDAKAMAASGTVAVLLPGAFYFLRETQLPPMEALR Sbjct: 241 SSLHGSSLAARYQALSADHLEFMTEDDAKAMAASGTVAVLLPGAFYFLRETQLPPMEALR 300 Query: 301 KHGVKIAVASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGVTIHAAQALGMAQTHGS 360 KHGVKIAVASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGVTIHAAQALGMAQTHGS Sbjct: 301 KHGVKIAVASDLNPGTSPALSLRLMLNMACTCFRMTPEEALAGVTIHAAQALGMAQTHGS 360 Query: 361 LEAGKVADFVAWHIDRPADLAYWLGGDLEKRVVRHGVEID 400 LEAGKVADFVAWHIDRPADLAYWLGGDLEKRVVRHGVEID Sbjct: 361 LEAGKVADFVAWHIDRPADLAYWLGGDLEKRVVRHGVEID 400 Lambda K H 0.320 0.133 0.395 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: 695 Number of extensions: 18 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: 400 Length of database: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate Pf6N2E2_3798 (Imidazolonepropionase (EC 3.5.2.7))
to HMM TIGR01224 (hutI: imidazolonepropionase (EC 3.5.2.7))
# 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/TIGR01224.hmm # target sequence database: /tmp/gapView.31540.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01224 [M=377] Accession: TIGR01224 Description: hutI: imidazolonepropionase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-152 492.4 0.0 4.4e-152 492.2 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3798 Imidazolonepropionase (EC 3.5.2. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3798 Imidazolonepropionase (EC 3.5.2.7) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 492.2 0.0 4.4e-152 4.4e-152 1 375 [. 21 396 .. 21 398 .. 0.99 Alignments for each domain: == domain 1 score: 492.2 bits; conditional E-value: 4.4e-152 TIGR01224 1 iedaailveegkiaaigqkaalpgeeaakiidleGklvvPGlvDpHtHlvfagdRvkefelklq 64 iedaai+ ++++i++ig++a+lp+ + + dl+G v+PGl+D+HtH vf+g+R+ efe++lq lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3798 21 IEDAAIVTQGKHIQWIGPRAELPTGDYPAVNDLKGAWVTPGLIDCHTHTVFGGNRSGEFEQRLQ 84 5899999999**************99999*********************************** PP TIGR01224 65 GasYleilaeGgGilstvratraAseeellkeaeerlkkllrsGtttlEvKsGYGLdleaElkm 128 G+sY+ei+a+GgGi stvratraAse+el+++a +rl +l+r G+tt+E+KsGYGLdl +E k+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3798 85 GVSYAEIAAAGGGIASTVRATRAASEDELFASAAKRLGSLMRDGVTTVEIKSGYGLDLASERKI 148 **************************************************************** PP TIGR01224 129 LrvikalkeelpvdvvttflgaHavPkevqededeyvdaileelipkvaeeklaeavDvFcekg 192 Lrvi++l +elpv+v +t+l+aHa+P+e++++ d+y+++i++e++p+ a e l++avD+Fce lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3798 149 LRVIRRLGAELPVSVRSTCLAAHALPPEYKDRADDYIEHICSEMLPALAAEGLVDAVDAFCEYL 212 **************************************************************** PP TIGR01224 193 vFsveqsrrilkaaqeaGlavklHaeelkalggaelaaklgavsadHleeasdedikalaeagt 256 +Fs++q++r++ aq+ Gl+vklHae+l++l g++laa+ +a+sadHle ++++d+ka+a++gt lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3798 213 AFSPAQVERVFITAQQLGLPVKLHAEQLSSLHGSSLAARYQALSADHLEFMTEDDAKAMAASGT 276 **************************************************************** PP TIGR01224 257 vavlLPgtaflLr.eaapparklidekvivalatDlnPgsspllslqlilslavtllkltaeea 319 vavlLPg++++Lr ++ pp+++l++++v +a+a+DlnPg+sp lsl+l+l++a+t +++t+eea lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3798 277 VAVLLPGAFYFLReTQLPPMEALRKHGVKIAVASDLNPGTSPALSLRLMLNMACTCFRMTPEEA 340 *************9999*********************************************** PP TIGR01224 320 laaatvnaAqalglgeekGtleeGkdadlvvlsaesyeeiaYrlgvnvveaviknG 375 la++t++aAqalg+++++G+le+Gk ad+v ++++ ++++aY+lg++ + v+ +G lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3798 341 LAGVTIHAAQALGMAQTHGSLEAGKVADFVAWHIDRPADLAYWLGGDLEKRVVRHG 396 ***********************************************999999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (377 nodes) Target sequences: 1 (400 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: 00:00:00.02 # Mc/sec: 7.23 // [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