Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate WP_013683509.1 ARCVE_RS04035 3-isopropylmalate dehydratase large subunit
Query= BRENDA::P81291 (424 letters) >NCBI__GCF_000194625.1:WP_013683509.1 Length = 418 Score = 481 bits (1238), Expect = e-140 Identities = 247/426 (57%), Positives = 314/426 (73%), Gaps = 11/426 (2%) Query: 1 MGMTIVEKILAKASGKKEVSPGDIVMANIDVAMVHDITGPLTVNTLKEYGIE--KVWNPE 58 MG TI EKIL++A+GK +V GD V+A+ID AMVHDIT PL + +E E KVW+P Sbjct: 1 MGKTIAEKILSRAAGK-DVKAGDYVLADIDRAMVHDITAPLAIKAFREIAGESAKVWDPS 59 Query: 59 KIVILFDHQVPADSIKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEVV 118 +I++ FDHQVPADS+ AAE H ++RKF +EQ I YD+ EG+ HQ++ EKGH PGE++ Sbjct: 60 RIIMAFDHQVPADSVTAAETHKMLRKFAEEQNILN-YDVHEGIAHQIMVEKGHAKPGELI 118 Query: 119 VGADSHTCTHGAFGAFATGIGSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTSKDVI 178 VGADSHTC +GA G FATGIGSTDM VFATGKLWF+VPETI F + G L+ +V SKD+I Sbjct: 119 VGADSHTCMYGALGCFATGIGSTDMGFVFATGKLWFRVPETIRFEVNGKLEKHVYSKDII 178 Query: 179 LSIIGEVGVDGATYKACQFGGETVKKMSIASRMTMTNMAIEMGGKTGIIEPDEKTIQYVK 238 L +IG VG DGA YKAC++ G+ V+KMS+A R+TM+NMAIEMGGK GIIEPD++T +Y++ Sbjct: 179 LKLIGMVGSDGANYKACEYAGDVVRKMSMAQRLTMSNMAIEMGGKAGIIEPDDETRKYLR 238 Query: 239 EAMKKHGTERPFEVIKGDEDAEFAEVYEIEADKIEPVFACPHNVDNVKQAREVAGKPIDQ 298 G E FE I GDEDAE A+ E++ +EP A PH VDNV EV G +DQ Sbjct: 239 AI----GVE-DFEEIHGDEDAE-AKTVELDVTGMEPQVAKPHRVDNVVGVSEVKGTKVDQ 292 Query: 299 VFIGSCTNGRLEDLRMAIKIIEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGC 358 VFIGSCTNGR EDL++A + + K IA +VR++V PASR EY KALK+G+I+ F++ G Sbjct: 293 VFIGSCTNGRYEDLKIAAEFL-KGEKIAKNVRLIVIPASRAEYRKALKDGLIDIFVEAGG 351 Query: 359 VVTNPSCSACMGSLYGVLGPGEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGEL 418 +V P C CMG +G++ GEV VSTSNRNF GRQGS E +IYL SP TAAA A+ GE+ Sbjct: 352 IVEFPCCGPCMGGSFGLIASGEVSVSTSNRNFIGRQGSPEGKIYLVSPATAAATALYGEI 411 Query: 419 VDPRDL 424 DPR++ Sbjct: 412 TDPREV 417 Lambda K H 0.318 0.136 0.400 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: 578 Number of extensions: 23 Number of successful extensions: 7 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: 424 Length of database: 418 Length adjustment: 32 Effective length of query: 392 Effective length of database: 386 Effective search space: 151312 Effective search space used: 151312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_013683509.1 ARCVE_RS04035 (3-isopropylmalate dehydratase large subunit)
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.17132.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-176 570.7 3.1 8.7e-176 570.5 3.1 1.0 1 lcl|NCBI__GCF_000194625.1:WP_013683509.1 ARCVE_RS04035 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013683509.1 ARCVE_RS04035 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 570.5 3.1 8.7e-176 8.7e-176 1 411 [] 3 416 .. 3 416 .. 0.99 Alignments for each domain: == domain 1 score: 570.5 bits; conditional E-value: 8.7e-176 TIGR02086 1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelg...akvekkekivlvfDhvvPa 66 kt+aekils+++Gk+vkaG+ v++ +D +mvhD t+pl+ika+re++ akv+++++i+++fDh+vPa lcl|NCBI__GCF_000194625.1:WP_013683509.1 3 KTIAEKILSRAAGKDVKAGDYVLADIDRAMVHDITAPLAIKAFREIAgesAKVWDPSRIIMAFDHQVPA 71 699*******************************************99999****************** PP TIGR02086 67 ptveaaelqkeirefakelgikvfdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGa 135 +v aae++k++r+fa e++i ++dv eGi+hq++vekg+akpg+++vgaDsht+ +Galg fatG+G+ lcl|NCBI__GCF_000194625.1:WP_013683509.1 72 DSVTAAETHKMLRKFAEEQNILNYDVHEGIAHQIMVEKGHAKPGELIVGADSHTCMYGALGCFATGIGS 140 ********************************************************************* PP TIGR02086 136 tDvalalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealslde 204 tD+ +++atGk+W++vPe+i+ e++Gkle++v++kD+il++++ +g+dga+yka e+ g++++++s+ + lcl|NCBI__GCF_000194625.1:WP_013683509.1 141 TDMGFVFATGKLWFRVPETIRFEVNGKLEKHVYSKDIILKLIGMVGSDGANYKACEYAGDVVRKMSMAQ 209 ********************************************************************* PP TIGR02086 205 Rltlsnlaveagakaglvepdeetleylkkrrge.frilkadedakyeeeieidlseleplvavPhsvd 272 Rlt+sn+a+e+g+kag++epd+et++yl++ e f++++ deda ++ +e+d++ +ep+va+Ph+vd lcl|NCBI__GCF_000194625.1:WP_013683509.1 210 RLTMSNMAIEMGGKAGIIEPDDETRKYLRAIGVEdFEEIHGDEDA-EAKTVELDVTGMEPQVAKPHRVD 277 *****************************9987769999999999.67889****************** PP TIGR02086 273 nvkeveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietl 341 nv v+ev+gt++dqvfiGsCtnGR+edlkiaae l+g++ +k+vrliv+Pasr y+kal++Gli+++ lcl|NCBI__GCF_000194625.1:WP_013683509.1 278 NVVGVSEVKGTKVDQVFIGSCTNGRYEDLKIAAEFLKGEKIAKNVRLIVIPASRAEYRKALKDGLIDIF 346 ********************************************************************* PP TIGR02086 342 veaGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdpe 410 veaG i+ p CGPC+G +G +a gev+vst+nRnf GR Gsp+ +iYL sPa+aa++a++Geitdp+ lcl|NCBI__GCF_000194625.1:WP_013683509.1 347 VEAGGIVEFPCCGPCMGGSFGLIASGEVSVSTSNRNFIGRQGSPEGKIYLVSPATAAATALYGEITDPR 415 ********************************************************************8 PP TIGR02086 411 e 411 e lcl|NCBI__GCF_000194625.1:WP_013683509.1 416 E 416 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (411 nodes) Target sequences: 1 (418 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: 00:00:00.02 # Mc/sec: 7.81 // [ok]
This GapMind analysis is from Apr 10 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