Align inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate GFF706 PGA1_c07210 inositol 2-dehydrogenase IdhA
Query= BRENDA::O68965 (330 letters) >FitnessBrowser__Phaeo:GFF706 Length = 328 Score = 348 bits (893), Expect = e-100 Identities = 176/319 (55%), Positives = 223/319 (69%) Query: 3 VRFGLLGAGRIGKVHAKAVSGNADARLVAVADAFPAAAEAIAGAYGCEVRTIDAIEAAAD 62 + GLLG GRIG+VHA++V R+ AVADA P AA A+A G +VR A+ +AD Sbjct: 2 LNIGLLGCGRIGQVHARSVGQLDGVRVTAVADAMPDAANALASKIGADVREASALITSAD 61 Query: 63 IDAVVICTPTDTHADLIERFARAGKAIFCEKPIDLDAERVRACLKVVSDTKAKLMVGFNR 122 +DAVVI TPTDTH DLI + A AGKAIFCEKP+D+ A+R+R C KVV++ + FNR Sbjct: 62 VDAVVIGTPTDTHYDLIHQAAAAGKAIFCEKPVDMSADRIRDCQKVVTEAGVAFLTAFNR 121 Query: 123 RFDPHFMAVRKAIDDGRIGEVEMVTITSRDPSAPPVDYIKRSGGIFRDMTIHDFDMARFL 182 RFDP+F +++ + G IG+VE+V+I SRDPS PP+ YIK SGG+FRDM IHDFDMARFL Sbjct: 122 RFDPNFANLQQRLRAGEIGDVEIVSILSRDPSPPPISYIKTSGGLFRDMMIHDFDMARFL 181 Query: 183 LGEEPVSVTATAAVLIDKAIGDAGDYDSVSVILQTASGKQAIISNSRRATYGYDQRIEVH 242 L EEPV V A + L+D AIG AGD D+ +V L T SGK ISNSRRATYGYDQR+EVH Sbjct: 182 LAEEPVQVFAVGSALVDPAIGAAGDVDTAAVTLTTTSGKICQISNSRRATYGYDQRVEVH 241 Query: 243 GSKGAVAAENQRPVSIEIATGDGYTRPPLHDFFMTRYTEAYANEIESFIAAIEKGAEIAP 302 GSKG + A N ++E+A G+ P FF+ RY AY NE+ F+ A++ G +P Sbjct: 242 GSKGMLRAANMLENTVEVAGTTGFQTAPAQHFFLERYEAAYRNEMARFVEAVQTGNTPSP 301 Query: 303 SGNDGLAALALADAAVRSV 321 S +DGL A LADAA +S+ Sbjct: 302 SIDDGLRAQMLADAAAQSL 320 Lambda K H 0.320 0.134 0.379 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: 316 Number of extensions: 11 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate GFF706 PGA1_c07210 (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.19923.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-135 437.0 0.3 2.1e-135 436.8 0.3 1.0 1 lcl|FitnessBrowser__Phaeo:GFF706 PGA1_c07210 inositol 2-dehydroge Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF706 PGA1_c07210 inositol 2-dehydrogenase IdhA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 436.8 0.3 2.1e-135 2.1e-135 1 329 [. 1 326 [. 1 327 [. 0.99 Alignments for each domain: == domain 1 score: 436.8 bits; conditional E-value: 2.1e-135 TIGR04380 1 klkigiiGaGRigkvHaenlakkvpeaelaavvdvaeeaakelaeklgieevvedveailedpevdAvliasptdtH 77 +l+ig++G GRig+vHa+++ + ++++++av+d+ +aa++la+k+g+ v++++a++++++vdAv+i +ptdtH lcl|FitnessBrowser__Phaeo:GFF706 1 MLNIGLLGCGRIGQVHARSVGQL-DGVRVTAVADAMPDAANALASKIGA--DVREASALITSADVDAVVIGTPTDTH 74 689*****************988.*************************..8999********************** PP TIGR04380 78 aeliveaakagkhifcEKPidldleeikealkavekagvklqiGfnRRFDanfaevkklveagkiGklellritsrD 154 ++li +aa+agk+ifcEKP+d++ ++i++++k+v +agv ++ fnRRFD+nfa+++++++ag+iG++e+++i srD lcl|FitnessBrowser__Phaeo:GFF706 75 YDLIHQAAAAGKAIFCEKPVDMSADRIRDCQKVVTEAGVAFLTAFNRRFDPNFANLQQRLRAGEIGDVEIVSILSRD 151 ***************************************************************************** PP TIGR04380 155 PapppveyvkvsGglflDmtiHDfDmarfllgseveevyaagsvlvdpeleeagdvdtavvvlkfengalaviensr 231 P+ppp++y+k+sGglf+Dm+iHDfDmarfll +e+++v+a+gs+lvdp+++ agdvdta+v+l + +g+++ i+nsr lcl|FitnessBrowser__Phaeo:GFF706 152 PSPPPISYIKTSGGLFRDMMIHDFDMARFLLAEEPVQVFAVGSALVDPAIGAAGDVDTAAVTLTTTSGKICQISNSR 228 ***************************************************************************** PP TIGR04380 232 raayGYdqrvEvfGskGslraendtestvvlsdeegvraekpenfFleRyaeayraeikafvdailedkevsvtaeD 308 ra+yGYdqrvEv+GskG+lra+n e+tv++++++g++++ ++fFleRy++ayr+e+++fv+a+++++++s++++D lcl|FitnessBrowser__Phaeo:GFF706 229 RATYGYDQRVEVHGSKGMLRAANMLENTVEVAGTTGFQTAPAQHFFLERYEAAYRNEMARFVEAVQTGNTPSPSIDD 305 ***************************************************************************** PP TIGR04380 309 glkalklalaakrsleegrav 329 gl+a++la+aa +sle+g +v lcl|FitnessBrowser__Phaeo:GFF706 306 GLRAQMLADAAAQSLETGAPV 326 *****************9998 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.47 // [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