Align Myo-inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate HSERO_RS12095 HSERO_RS12095 myo-inositol 2-dehydrogenase
Query= reanno::HerbieS:HSERO_RS12095 (330 letters) >FitnessBrowser__HerbieS:HSERO_RS12095 Length = 330 Score = 642 bits (1657), Expect = 0.0 Identities = 330/330 (100%), Positives = 330/330 (100%) Query: 1 MIDVAIFGAGRIGKIHAANIAAQAGVRLKYVCDVHAESAAELAQRHGAQVGRVEQVLDDS 60 MIDVAIFGAGRIGKIHAANIAAQAGVRLKYVCDVHAESAAELAQRHGAQVGRVEQVLDDS Sbjct: 1 MIDVAIFGAGRIGKIHAANIAAQAGVRLKYVCDVHAESAAELAQRHGAQVGRVEQVLDDS 60 Query: 61 SVAAVVIASSTDTHADLILRAAAAGKAIFCEKPVDLDLQRAQACAEAVRAAGVTCMIGFQ 120 SVAAVVIASSTDTHADLILRAAAAGKAIFCEKPVDLDLQRAQACAEAVRAAGVTCMIGFQ Sbjct: 61 SVAAVVIASSTDTHADLILRAAAAGKAIFCEKPVDLDLQRAQACAEAVRAAGVTCMIGFQ 120 Query: 121 RRFDPTFESLSRRLEAGEIGDPEMLLVTSRDPGAPPLSYIASSGGIFKDMLIHDFDIFRW 180 RRFDPTFESLSRRLEAGEIGDPEMLLVTSRDPGAPPLSYIASSGGIFKDMLIHDFDIFRW Sbjct: 121 RRFDPTFESLSRRLEAGEIGDPEMLLVTSRDPGAPPLSYIASSGGIFKDMLIHDFDIFRW 180 Query: 181 ILADEAVSVFATGSCLTDPAIATAGDVDSTAVTLTTRSGRLCQINTSRRAAYGYDQRFEV 240 ILADEAVSVFATGSCLTDPAIATAGDVDSTAVTLTTRSGRLCQINTSRRAAYGYDQRFEV Sbjct: 181 ILADEAVSVFATGSCLTDPAIATAGDVDSTAVTLTTRSGRLCQINTSRRAAYGYDQRFEV 240 Query: 241 LGSKGMLQAGNHRPTEVVAATASQVGSDLPEHFFLERYRAAYAREMAHFFQAMQSGAPVR 300 LGSKGMLQAGNHRPTEVVAATASQVGSDLPEHFFLERYRAAYAREMAHFFQAMQSGAPVR Sbjct: 241 LGSKGMLQAGNHRPTEVVAATASQVGSDLPEHFFLERYRAAYAREMAHFFQAMQSGAPVR 300 Query: 301 TSIEDGVKALQLAEAAATSWRERRIVSLSA 330 TSIEDGVKALQLAEAAATSWRERRIVSLSA Sbjct: 301 TSIEDGVKALQLAEAAATSWRERRIVSLSA 330 Lambda K H 0.321 0.132 0.380 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: 482 Number of extensions: 6 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: 330 Length of database: 330 Length adjustment: 28 Effective length of query: 302 Effective length of database: 302 Effective search space: 91204 Effective search space used: 91204 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: 49 (23.5 bits)
Align candidate HSERO_RS12095 HSERO_RS12095 (myo-inositol 2-dehydrogenase)
to HMM TIGR04380 (iolG: inositol 2-dehydrogenase (EC 1.1.1.18))
# 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/TIGR04380.hmm # target sequence database: /tmp/gapView.2999.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04380 [M=330] Accession: TIGR04380 Description: myo_inos_iolG: inositol 2-dehydrogenase 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-132 424.8 0.6 1.1e-131 424.6 0.6 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS12095 HSERO_RS12095 myo-inositol 2-deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS12095 HSERO_RS12095 myo-inositol 2-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 424.6 0.6 1.1e-131 1.1e-131 1 329 [. 1 326 [. 1 327 [. 0.99 Alignments for each domain: == domain 1 score: 424.6 bits; conditional E-value: 1.1e-131 TIGR04380 1 klkigiiGaGRigkvHaenlakkvpeaelaavvdvaeeaakelaeklgieevvedveailedpevdAv 68 +++++i+GaGRigk+Ha n+a++ +++l++v+dv++e+a+ela++ g+ +v ve++l+d+ v Av lcl|FitnessBrowser__HerbieS:HSERO_RS12095 1 MIDVAIFGAGRIGKIHAANIAAQ-AGVRLKYVCDVHAESAAELAQRHGA--QVGRVEQVLDDSSVAAV 65 689********************.*************************..8999************* PP TIGR04380 69 liasptdtHaeliveaakagkhifcEKPidldleeikealkavekagvklqiGfnRRFDanfaevkkl 136 +ias+tdtHa+li +aa+agk+ifcEKP+dldl++++++++av++agv ++iGf+RRFD++f+++ ++ lcl|FitnessBrowser__HerbieS:HSERO_RS12095 66 VIASSTDTHADLILRAAAAGKAIFCEKPVDLDLQRAQACAEAVRAAGVTCMIGFQRRFDPTFESLSRR 133 ******************************************************************** PP TIGR04380 137 veagkiGklellritsrDPapppveyvkvsGglflDmtiHDfDmarfllgseveevyaagsvlvdpel 204 +eag+iG++e+l +tsrDP +pp +y+++sGg+f Dm iHDfD+ r++l +e ++v+a+gs+l dp++ lcl|FitnessBrowser__HerbieS:HSERO_RS12095 134 LEAGEIGDPEMLLVTSRDPGAPPLSYIASSGGIFKDMLIHDFDIFRWILADEAVSVFATGSCLTDPAI 201 ******************************************************************** PP TIGR04380 205 eeagdvdtavvvlkfengalaviensrraayGYdqrvEvfGskGslraendtestvvlsdeegvraek 272 + agdvd+++v+l +++g+l+ i+ srraayGYdqr Ev+GskG+l+a n+++++vv +++++v ++ lcl|FitnessBrowser__HerbieS:HSERO_RS12095 202 ATAGDVDSTAVTLTTRSGRLCQINTSRRAAYGYDQRFEVLGSKGMLQAGNHRPTEVVAATASQVGSDL 269 ******************************************************************** PP TIGR04380 273 penfFleRyaeayraeikafvdailedkevsvtaeDglkalklalaakrsleegrav 329 pe+fFleRy++ay++e+++f++a++++++v ++eDg+kal+la+aa s +e+r+v lcl|FitnessBrowser__HerbieS:HSERO_RS12095 270 PEHFFLERYRAAYAREMAHFFQAMQSGAPVRTSIEDGVKALQLAEAAATSWRERRIV 326 *****************************************************9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (330 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: 00:00:00.01 # Mc/sec: 8.35 // [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