Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate H281DRAFT_04457 H281DRAFT_04457 2-keto-myo-inositol dehydratase
Query= reanno::BFirm:BPHYT_RS13920 (305 letters) >FitnessBrowser__Burk376:H281DRAFT_04457 Length = 316 Score = 578 bits (1491), Expect = e-170 Identities = 287/316 (90%), Positives = 297/316 (93%), Gaps = 11/316 (3%) Query: 1 MTAFDVRIGINPLSWMNDDLPSLGGETPLEVALTEGREIGYQGFELGNKFPREPQALKSL 60 MTAF+VRIGINPLSWMNDDLPSLGGETPLE+ALTEGREIGYQGFELGNKFPREPQALK+L Sbjct: 1 MTAFNVRIGINPLSWMNDDLPSLGGETPLELALTEGREIGYQGFELGNKFPREPQALKTL 60 Query: 61 LAQYDLALVSGWYSGRLARRSVEEEIAEVGPHLELLAQNGATAMVYGEVADSIQGAAQPL 120 LAQYDLALVSGWYSGRLARRSVEEEIAEVGPHLELLA+NGAT MVYGEVADSIQGA +PL Sbjct: 61 LAQYDLALVSGWYSGRLARRSVEEEIAEVGPHLELLARNGATVMVYGEVADSIQGAPRPL 120 Query: 121 YQRPRFFSEKQWADYAARVDEFARYTLSRGVRLAYHHHMGAYVETPADVDQLMARTSDAV 180 YQRPRFFS+ QWA YAARVDEFARYTLSRGVRLAYHHHMGAYVETPADVDQLM+RTSDAV Sbjct: 121 YQRPRFFSDAQWAAYAARVDEFARYTLSRGVRLAYHHHMGAYVETPADVDQLMSRTSDAV 180 Query: 181 GLLFDAGHITFAGGDPLAVLDKHIGRVCHVHCKDVRPAVMKLARNRNWSFLDAVIAGAFT 240 GLLFDAGHITFAGGDPL VLDKHIGRVCHVHCKDVRPAVMKLARNRNWSFLDAVIAGAFT Sbjct: 181 GLLFDAGHITFAGGDPLVVLDKHIGRVCHVHCKDVRPAVMKLARNRNWSFLDAVIAGAFT 240 Query: 241 VPGDGAVNFPAIIERLKRHGYCGWLVVEAEQDPVVAPSFEYAQKGYKTLRALVDAPLD-- 298 VPGDGAV+FP+II RLKRHGY GWLVVEAEQDPVVAPSFEYAQKGY+TLRALVDAPLD Sbjct: 241 VPGDGAVDFPSIIARLKRHGYSGWLVVEAEQDPVVAPSFEYAQKGYQTLRALVDAPLDTT 300 Query: 299 ---------GTEQEAA 305 GT QEAA Sbjct: 301 SAGTRGDSHGTTQEAA 316 Lambda K H 0.320 0.137 0.417 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: 460 Number of extensions: 7 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: 305 Length of database: 316 Length adjustment: 27 Effective length of query: 278 Effective length of database: 289 Effective search space: 80342 Effective search space used: 80342 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: 48 (23.1 bits)
Align candidate H281DRAFT_04457 H281DRAFT_04457 (2-keto-myo-inositol dehydratase)
to HMM TIGR04379 (iolE: myo-inosose-2 dehydratase (EC 4.2.1.44))
# 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/TIGR04379.hmm # target sequence database: /tmp/gapView.10846.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04379 [M=290] Accession: TIGR04379 Description: myo_inos_iolE: myo-inosose-2 dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-125 404.1 0.0 2.2e-125 404.0 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04457 H281DRAFT_04457 2-keto-myo-inosi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04457 H281DRAFT_04457 2-keto-myo-inositol dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 404.0 0.0 2.2e-125 2.2e-125 1 289 [. 5 292 .. 5 293 .. 0.98 Alignments for each domain: == domain 1 score: 404.0 bits; conditional E-value: 2.2e-125 TIGR04379 1 kvklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvs 66 +v++gi+P++W+ndDlp+lgg+t+le +l+e +e+g++g+Elgnkfp++p++Lk++l +++l+lvs lcl|FitnessBrowser__Burk376:H281DRAFT_04457 5 NVRIGINPLSWMNDDLPSLGGETPLELALTEGREIGYQGFELGNKFPREPQALKTLLAQYDLALVS 70 599*************************************************************** PP TIGR04379 67 gwfsallleksveeeieavrehlellkalgakvivvaEvgksiqgdkdtplaerpkl.teeeweel 131 gw+s++l+++sveeei++v hlell+ ga+v+v++Ev++siqg +pl +rp++ ++++w+++ lcl|FitnessBrowser__Burk376:H281DRAFT_04457 71 GWYSGRLARRSVEEEIAEVGPHLELLARNGATVMVYGEVADSIQGA-PRPLYQRPRFfSDAQWAAY 135 *********************************************9.899****66549******* PP TIGR04379 132 aeklnklgeilkekglklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavl 197 a+++++++++ ++g++layHhH+g++vet +++d+lm+ t+++ vgll+D+GH++fag+dpl vl lcl|FitnessBrowser__Burk376:H281DRAFT_04457 136 AARVDEFARYTLSRGVRLAYHHHMGAYVETPADVDQLMSRTSDA-VGLLFDAGHITFAGGDPLVVL 200 ******************************************99.********************* PP TIGR04379 198 ekyadRiahvHlKDvRkevleevrkekksFldavlkGvftvPGdGcidfeeilealkakdYeGWlv 263 +k++ R++hvH+KDvR++v++ +r++++sFldav++G+ftvPGdG++df +i++ lk+++Y+GWlv lcl|FitnessBrowser__Burk376:H281DRAFT_04457 201 DKHIGRVCHVHCKDVRPAVMKLARNRNWSFLDAVIAGAFTVPGDGAVDFPSIIARLKRHGYSGWLV 266 ****************************************************************** PP TIGR04379 264 vEaEqDPakaepleyakkakkyleel 289 vEaEqDP +a+++eya+k++++l++l lcl|FitnessBrowser__Burk376:H281DRAFT_04457 267 VEAEQDPVVAPSFEYAQKGYQTLRAL 292 **********************9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (290 nodes) Target sequences: 1 (316 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 4.42 // [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