Align Myo-inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate CCNA_01354 CCNA_01354 myo-inositol 2-dehydrogenase IdhA
Query= reanno::HerbieS:HSERO_RS12095 (330 letters) >FitnessBrowser__Caulo:CCNA_01354 Length = 328 Score = 329 bits (843), Expect = 7e-95 Identities = 168/328 (51%), Positives = 218/328 (66%) Query: 1 MIDVAIFGAGRIGKIHAANIAAQAGVRLKYVCDVHAESAAELAQRHGAQVGRVEQVLDDS 60 M D+AI GAGRIG+IHA N+A+Q G+RLKYV D A +A LA GA V +E L+D Sbjct: 1 MHDIAILGAGRIGRIHAKNVASQPGLRLKYVVDPVAAAADGLAGETGASVADLETALNDP 60 Query: 61 SVAAVVIASSTDTHADLILRAAAAGKAIFCEKPVDLDLQRAQACAEAVRAAGVTCMIGFQ 120 +VA V++ASSTDTH D L+A AAGKA+FCEKP+D DL RA++ + + GV +GF Sbjct: 61 AVAGVIVASSTDTHLDYSLKAIAAGKAVFCEKPIDQDLARARSASGELGGKGVKLFLGFN 120 Query: 121 RRFDPTFESLSRRLEAGEIGDPEMLLVTSRDPGAPPLSYIASSGGIFKDMLIHDFDIFRW 180 RRFDP F+ L RL AG +G E + +TS DP PP+SY+ SGG+FKDM IHDFD+ RW Sbjct: 121 RRFDPNFQGLKARLSAGVVGALETVHITSHDPAPPPVSYVKVSGGLFKDMTIHDFDMARW 180 Query: 181 ILADEAVSVFATGSCLTDPAIATAGDVDSTAVTLTTRSGRLCQINTSRRAAYGYDQRFEV 240 +L + VFA SCL DPAI AGDVD+ + L T SG++C I+ SRR+ YGYDQR E Sbjct: 181 LLDEPVSEVFAAASCLVDPAIGEAGDVDTAKILLRTASGKICMISNSRRSGYGYDQRIEA 240 Query: 241 LGSKGMLQAGNHRPTEVVAATASQVGSDLPEHFFLERYRAAYAREMAHFFQAMQSGAPVR 300 GSKG+++A N + V + SD ++FFL+RY AY REMAHF + ++ A Sbjct: 241 FGSKGLVRADNVMESTVSIWGENGAASDAFQNFFLDRYAEAYRREMAHFAEIIRGEALPS 300 Query: 301 TSIEDGVKALQLAEAAATSWRERRIVSL 328 DGV+AL LAEAA S + ++V L Sbjct: 301 VGYVDGVEALALAEAAGLSAKTGQVVKL 328 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: 313 Number of extensions: 12 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: 328 Length adjustment: 28 Effective length of query: 302 Effective length of database: 300 Effective search space: 90600 Effective search space used: 90600 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 CCNA_01354 CCNA_01354 (myo-inositol 2-dehydrogenase IdhA)
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.2883.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-136 440.0 0.0 2.4e-136 439.9 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_01354 CCNA_01354 myo-inositol 2-dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_01354 CCNA_01354 myo-inositol 2-dehydrogenase IdhA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 439.9 0.0 2.4e-136 2.4e-136 2 330 .] 2 327 .. 1 327 [. 0.99 Alignments for each domain: == domain 1 score: 439.9 bits; conditional E-value: 2.4e-136 TIGR04380 2 lkigiiGaGRigkvHaenlakkvpeaelaavvdvaeeaakelaeklgieevvedveailedpevdAvliaspt 74 ++i+i+GaGRig++Ha+n+a++ p+++l++vvd++++aa+ la ++g+ v+d+e++l+dp v +v++as+t lcl|FitnessBrowser__Caulo:CCNA_01354 2 HDIAILGAGRIGRIHAKNVASQ-PGLRLKYVVDPVAAAADGLAGETGA--SVADLETALNDPAVAGVIVASST 71 68********************.*************************..99********************* PP TIGR04380 75 dtHaeliveaakagkhifcEKPidldleeikealkavekagvklqiGfnRRFDanfaevkklveagkiGklel 147 dtH++++ +a++agk++fcEKPid+dl+++++a ++ +gvkl++GfnRRFD+nf+ +k++++ag +G+le+ lcl|FitnessBrowser__Caulo:CCNA_01354 72 DTHLDYSLKAIAAGKAVFCEKPIDQDLARARSASGELGGKGVKLFLGFNRRFDPNFQGLKARLSAGVVGALET 144 ************************************************************************* PP TIGR04380 148 lritsrDPapppveyvkvsGglflDmtiHDfDmarfllgseveevyaagsvlvdpeleeagdvdtavvvlkfe 220 ++its+DPapppv+yvkvsGglf DmtiHDfDmar+ll++ v+ev+aa+s+lvdp+++eagdvdta ++l+++ lcl|FitnessBrowser__Caulo:CCNA_01354 145 VHITSHDPAPPPVSYVKVSGGLFKDMTIHDFDMARWLLDEPVSEVFAAASCLVDPAIGEAGDVDTAKILLRTA 217 ************************************************************************* PP TIGR04380 221 ngalaviensrraayGYdqrvEvfGskGslraendtestvvlsdeegvraekpenfFleRyaeayraeikafv 293 +g++++i+nsrr+ yGYdqr+E+fGskG +ra+n++estv++++e+g ++++ +nfFl+Ryaeayr+e+++f+ lcl|FitnessBrowser__Caulo:CCNA_01354 218 SGKICMISNSRRSGYGYDQRIEAFGSKGLVRADNVMESTVSIWGENGAASDAFQNFFLDRYAEAYRREMAHFA 290 ************************************************************************* PP TIGR04380 294 dailedkevsvtaeDglkalklalaakrsleegravk 330 ++i+ ++ +sv++ Dg++al+la+aa s+++g++vk lcl|FitnessBrowser__Caulo:CCNA_01354 291 EIIRGEALPSVGYVDGVEALALAEAAGLSAKTGQVVK 327 **********************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (328 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 6.28 // [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