Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate 208495 DVU2982 3-isopropylmalate dehydratase, large subunit, putative
Query= reanno::DvH:208495 (419 letters) >MicrobesOnline__882:208495 Length = 419 Score = 832 bits (2150), Expect = 0.0 Identities = 419/419 (100%), Positives = 419/419 (100%) Query: 1 MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60 MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV Sbjct: 1 MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60 Query: 61 ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120 ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV Sbjct: 61 ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120 Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL Sbjct: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180 Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT Sbjct: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240 Query: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC Sbjct: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300 Query: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC Sbjct: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360 Query: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL Sbjct: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419 Lambda K H 0.320 0.136 0.401 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: 825 Number of extensions: 22 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: 419 Length of database: 419 Length adjustment: 32 Effective length of query: 387 Effective length of database: 387 Effective search space: 149769 Effective search space used: 149769 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: 50 (23.9 bits)
Align candidate 208495 DVU2982 (3-isopropylmalate dehydratase, large subunit, putative)
to HMM TIGR02086 (3-isopropylmalate dehydratase, large subunit)
# 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.aa/TIGR02086.hmm # target sequence database: /tmp/gapView.25546.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02086 [M=411] Accession: TIGR02086 Description: IPMI_arch: 3-isopropylmalate dehydratase, large subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-159 516.3 1.2 2.9e-159 516.1 1.2 1.0 1 lcl|MicrobesOnline__882:208495 DVU2982 3-isopropylmalate dehydr Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:208495 DVU2982 3-isopropylmalate dehydratase, large subunit, putative # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 516.1 1.2 2.9e-159 2.9e-159 2 410 .. 4 417 .. 3 418 .. 0.98 Alignments for each domain: == domain 1 score: 516.1 bits; conditional E-value: 2.9e-159 TIGR02086 2 tlaekilsekvGke.vkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPaptveaaelqkei 78 tla+kil +++ + aG+iv +v +v+++D t+pl+ik++r +g ++v++k+++ lv+Dh +P +++eaa+ k + lcl|MicrobesOnline__882:208495 4 TLAQKILQRHTDEAiTDAGQIVRCRVSMVLANDITAPLAIKSFRAMGaKRVFDKDRVALVMDHFTPQKDIEAAQQVKLT 82 9***********994579*****************************899***************************** PP TIGR02086 79 refakelgikv.fdv.geGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatDvalalatGktWlkvPesi 155 refa+e+g+++ ++ + G+ h +l e g++ pg+vvvgaDsht+t+G+lgafatGlG+tDva a+a+G+tW+kvP +i lcl|MicrobesOnline__882:208495 83 REFAREMGVTHyYEGgDCGVEHALLPELGLVGPGDVVVGADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTI 161 ***********7665156************************************************************* PP TIGR02086 156 kveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeRltlsnlaveagakaglvepdeetleylkk 234 + +++G l +v akD+il++++ +g dga y+a+ef g ieal++++R+t++n+a+eag+kagl+ +d +tl y + lcl|MicrobesOnline__882:208495 162 RATFTGTLPAYVGAKDLILTLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240 *****************************************************************************99 PP TIGR02086 235 rrge.frilkadedakyeeeieidlseleplvavPhsvdnvkeveevegteidqvfiGsCtnGRledlkiaaeilegre 312 ++ ++ad +a ye e+ +d++ ++p+va+Ph +dnvk+v+ev+ ++++qv iGsCtnGR+ dl++aa +l+gr+ lcl|MicrobesOnline__882:208495 241 AGRTgDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSCTNGRIGDLREAAAVLRGRK 319 9888777899********************************************************************* PP TIGR02086 313 vhkdvrlivvPasrkvyekaleeGlietlveaGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYL 391 v +dvr+iv Pa ++++al+eGliet++eaG+i+ + +CGPClG h+G+ladge+ ++ttnRnfkGRmGs ++e+YL lcl|MicrobesOnline__882:208495 320 VSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATCGPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYL 398 ******************************************************************************* PP TIGR02086 392 asPavaavsaveGeitdpe 410 ++Pa+aa+sav+G+itdp lcl|MicrobesOnline__882:208495 399 SGPATAAASAVTGVITDPS 417 *****************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (411 nodes) Target sequences: 1 (419 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: 12.13 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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