Align Myo-inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate H281DRAFT_04464 H281DRAFT_04464 myo-inositol 2-dehydrogenase
Query= reanno::HerbieS:HSERO_RS12095 (330 letters) >FitnessBrowser__Burk376:H281DRAFT_04464 Length = 339 Score = 481 bits (1239), Expect = e-141 Identities = 238/327 (72%), Positives = 276/327 (84%) Query: 2 IDVAIFGAGRIGKIHAANIAAQAGVRLKYVCDVHAESAAELAQRHGAQVGRVEQVLDDSS 61 IDVA+FGAGRIGKIHAAN+A Q GVRLKYV DV++E+AA LA HGA+V ++ + D+S Sbjct: 8 IDVAVFGAGRIGKIHAANLARQPGVRLKYVVDVNSEAAAALAAAHGAKVADIDGAMGDAS 67 Query: 62 VAAVVIASSTDTHADLILRAAAAGKAIFCEKPVDLDLQRAQACAEAVRAAGVTCMIGFQR 121 V A VI SSTDTHADLI+++AA K +FCEKPVDL L+RA+ACA+AV AGV CMIGFQR Sbjct: 68 VGATVICSSTDTHADLIMKSAAQKKHVFCEKPVDLTLERARACADAVERAGVVCMIGFQR 127 Query: 122 RFDPTFESLSRRLEAGEIGDPEMLLVTSRDPGAPPLSYIASSGGIFKDMLIHDFDIFRWI 181 RFDPTF +L RL+AGEIG PEML+VTSRDPGAPP+ YI SGGIFKDMLIHDFDIFRWI Sbjct: 128 RFDPTFSALKARLDAGEIGTPEMLVVTSRDPGAPPVDYIRHSGGIFKDMLIHDFDIFRWI 187 Query: 182 LADEAVSVFATGSCLTDPAIATAGDVDSTAVTLTTRSGRLCQINTSRRAAYGYDQRFEVL 241 L DEA ++ ATGSCL+DPAIA AGD+DSTAVT+ T+ GRLCQINT+RRAAYGYDQRFEVL Sbjct: 188 LGDEADTLHATGSCLSDPAIAEAGDIDSTAVTIRTKRGRLCQINTARRAAYGYDQRFEVL 247 Query: 242 GSKGMLQAGNHRPTEVVAATASQVGSDLPEHFFLERYRAAYAREMAHFFQAMQSGAPVRT 301 GS GMLQAGN RPTEV A + +QV SD+PE FFLERYRAAYA E+AHFF+A+ G PVRT Sbjct: 248 GSAGMLQAGNVRPTEVTAYSRTQVSSDVPEAFFLERYRAAYALEIAHFFEAVTQGKPVRT 307 Query: 302 SIEDGVKALQLAEAAATSWRERRIVSL 328 ++ DG+KAL+LAEAA SWRE R V L Sbjct: 308 TVADGLKALELAEAATRSWREGRAVKL 334 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: 379 Number of extensions: 10 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: 339 Length adjustment: 28 Effective length of query: 302 Effective length of database: 311 Effective search space: 93922 Effective search space used: 93922 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 H281DRAFT_04464 H281DRAFT_04464 (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.20014.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-129 416.0 0.4 5.1e-129 415.8 0.4 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04464 H281DRAFT_04464 myo-inositol 2-d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04464 H281DRAFT_04464 myo-inositol 2-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.8 0.4 5.1e-129 5.1e-129 2 330 .] 8 333 .. 7 333 .. 0.99 Alignments for each domain: == domain 1 score: 415.8 bits; conditional E-value: 5.1e-129 TIGR04380 2 lkigiiGaGRigkvHaenlakkvpeaelaavvdvaeeaakelaeklgieevvedveailedpevdA 67 ++++++GaGRigk+Ha nla++ p+++l++vvdv++eaa++la++ g+ +v+d++ ++ d+ v A lcl|FitnessBrowser__Burk376:H281DRAFT_04464 8 IDVAVFGAGRIGKIHAANLARQ-PGVRLKYVVDVNSEAAAALAAAHGA--KVADIDGAMGDASVGA 70 689*******************.*************************..999************* PP TIGR04380 68 vliasptdtHaeliveaakagkhifcEKPidldleeikealkavekagvklqiGfnRRFDanfaev 133 +i+s+tdtHa+li+++a+++kh+fcEKP+dl+le+++++++ave+agv ++iGf+RRFD++f+++ lcl|FitnessBrowser__Burk376:H281DRAFT_04464 71 TVICSSTDTHADLIMKSAAQKKHVFCEKPVDLTLERARACADAVERAGVVCMIGFQRRFDPTFSAL 136 ****************************************************************** PP TIGR04380 134 kklveagkiGklellritsrDPapppveyvkvsGglflDmtiHDfDmarfllgseveevyaagsvl 199 k++++ag+iG++e+l +tsrDP +ppv+y+++sGg+f Dm iHDfD+ r++lg+e + +a+gs+l lcl|FitnessBrowser__Burk376:H281DRAFT_04464 137 KARLDAGEIGTPEMLVVTSRDPGAPPVDYIRHSGGIFKDMLIHDFDIFRWILGDEADTLHATGSCL 202 ****************************************************************** PP TIGR04380 200 vdpeleeagdvdtavvvlkfengalaviensrraayGYdqrvEvfGskGslraendtestvvlsde 265 dp+++eagd+d+++v+++++ g+l+ i+ +rraayGYdqr Ev+Gs+G+l+a n+++++v+ +++ lcl|FitnessBrowser__Burk376:H281DRAFT_04464 203 SDPAIAEAGDIDSTAVTIRTKRGRLCQINTARRAAYGYDQRFEVLGSAGMLQAGNVRPTEVTAYSR 268 ****************************************************************** PP TIGR04380 266 egvraekpenfFleRyaeayraeikafvdailedkevsvtaeDglkalklalaakrsleegravk 330 ++v+++ pe fFleRy++ay+ ei++f++a++++k+v t+ Dglkal+la+aa+rs +egravk lcl|FitnessBrowser__Burk376:H281DRAFT_04464 269 TQVSSDVPEAFFLERYRAAYALEIAHFFEAVTQGKPVRTTVADGLKALELAEAATRSWREGRAVK 333 **************************************************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (339 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: 00:00:00.01 # Mc/sec: 8.45 // [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