Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate WP_084057448.1 B9A12_RS08400 3-isopropylmalate dehydratase large subunit
Query= BRENDA::P81291 (424 letters) >NCBI__GCF_900176285.1:WP_084057448.1 Length = 424 Score = 374 bits (959), Expect = e-108 Identities = 182/422 (43%), Positives = 272/422 (64%), Gaps = 7/422 (1%) Query: 3 MTIVEKILAKASGKKEVSPGDIVMANIDVAMVHDITGPLTVNTLKEYGIEKVWNPEKIVI 62 M +EKILA+A+GK+ V G+I+ +D+A V+D+ P T+ + +E G ++V +PE+I Sbjct: 1 MHAIEKILARAAGKESVRAGEIINCRVDLAEVNDLY-PQTILSFREMGGKRVHSPERIAF 59 Query: 63 LFDHQVPADSIKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEVVVGAD 122 + DH PA +++ AEN MR+F +EQGI+ +D+ GVCHQV+ + G V PG V++ D Sbjct: 60 ILDHYAPASTVQQAENQKFMRQFCREQGIELLFDVNSGVCHQVMVDHGLVYPGMVLIATD 119 Query: 123 SHTCTHGAFGAFATGIGSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTSKDVILSII 182 SHT THGAFGAF TG+G+TD+A + ATG LW +VPE I ++TG L V +KDVIL II Sbjct: 120 SHTTTHGAFGAFGTGVGATDLAVIMATGHLWLRVPEVIRIHLTGRLPLGVYAKDVILYII 179 Query: 183 GEVGVDGATYKACQFGGETVKKMSIASRMTMTNMAIEMGGKTGIIEPDEKTIQYVKEAMK 242 G++G D A YKA +F G VK +S++ RM + NM EMG K I+PDE T+ ++K ++ Sbjct: 180 GKLGADYAIYKAVEFTGPVVKALSVSERMALCNMTTEMGAKCAYIQPDEVTLDFLKGKVR 239 Query: 243 KHGTERPFEVIKGDEDAEFAEVYEIEADKIEPVFACPHNVDNVKQAREVAGKPIDQVFIG 302 R E + D D ++AE + + P A P +VDNV+ E+ G P+ Q ++G Sbjct: 240 -----RKLEPVVTDPDFQYAEELFFDVSAVSPQLAVPSSVDNVRPLSELVGTPVHQAYLG 294 Query: 303 SCTNGRLEDLRMAIKIIEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGCVVTN 362 SCT GR ED+ +A +I+ K + + R+VV PASR+ +L+AL+ G + ++ G Sbjct: 295 SCTGGRAEDIAVAARIL-KGRKVHKNTRLVVVPASRDVFLEALERGDVATLVEAGATFVT 353 Query: 363 PSCSACMGSLYGVLGPGEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGELVDPR 422 P C+AC+G+ G+L GE C++++NRNF GR G ++ +YL SP AA A+ GE+ DP Sbjct: 354 PGCAACLGTHEGILAAGETCIASTNRNFPGRMGHTQSAVYLGSPAAVAAAALNGEVTDPS 413 Query: 423 DL 424 + Sbjct: 414 QI 415 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: 512 Number of extensions: 17 Number of successful extensions: 4 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: 424 Length adjustment: 32 Effective length of query: 392 Effective length of database: 392 Effective search space: 153664 Effective search space used: 153664 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: 51 (24.3 bits)
Align candidate WP_084057448.1 B9A12_RS08400 (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.28194.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-160 520.0 0.5 2.1e-160 519.9 0.5 1.0 1 lcl|NCBI__GCF_900176285.1:WP_084057448.1 B9A12_RS08400 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084057448.1 B9A12_RS08400 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 519.9 0.5 2.1e-160 2.1e-160 3 410 .. 3 413 .. 1 414 [. 0.98 Alignments for each domain: == domain 1 score: 519.9 bits; conditional E-value: 2.1e-160 TIGR02086 3 laekilsekvGke.vkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPaptv 69 +ekil++++Gke v+aGei+ +vDl+ v+D p++i ++re+g ++v+++e+i ++Dh +Pa+tv lcl|NCBI__GCF_900176285.1:WP_084057448.1 3 AIEKILARAAGKEsVRAGEIINCRVDLAEVNDLY-PQTILSFREMGgKRVHSPERIAFILDHYAPASTV 70 579********988******************86.6677789999999********************* PP TIGR02086 70 eaaelqkeirefakelgikv.fdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatD 137 + ae qk +r+f +e+gi+ fdv++G+chqv+v++g++ pg+v++++Dshttt+Ga+gaf+tG+GatD lcl|NCBI__GCF_900176285.1:WP_084057448.1 71 QQAENQKFMRQFCREQGIELlFDVNSGVCHQVMVDHGLVYPGMVLIATDSHTTTHGAFGAFGTGVGATD 139 ********************9************************************************ PP TIGR02086 138 valalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeRl 206 +a+++atG++Wl+vPe i+++l+G+l v+akDvil i+++lgad+a yka+eftg +++als++eR+ lcl|NCBI__GCF_900176285.1:WP_084057448.1 140 LAVIMATGHLWLRVPEVIRIHLTGRLPLGVYAKDVILYIIGKLGADYAIYKAVEFTGPVVKALSVSERM 208 ********************************************************************* PP TIGR02086 207 tlsnlaveagakaglvepdeetleylkkrrge.frilkadedakyeeeieidlseleplvavPhsvdnv 274 +l+n+++e+gak ++++pde tl++lk ++++ + +++d+d +y+ee+ +d+s++ p+ avP svdnv lcl|NCBI__GCF_900176285.1:WP_084057448.1 209 ALCNMTTEMGAKCAYIQPDEVTLDFLKGKVRRkLEPVVTDPDFQYAEELFFDVSAVSPQLAVPSSVDNV 277 ***************************98877688899******************************* PP TIGR02086 275 keveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietlve 343 ++++e gt + q+++GsCt GR ed+ +aa+il+gr+vhk+ rl+vvPasr+v+ +ale+G + tlve lcl|NCBI__GCF_900176285.1:WP_084057448.1 278 RPLSELVGTPVHQAYLGSCTGGRAEDIAVAARILKGRKVHKNTRLVVVPASRDVFLEALERGDVATLVE 346 ********************************************************************* PP TIGR02086 344 aGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdpe 410 aGa+ +tpgC ClG+h G+la ge++++ tnRnf GRmG++++ +YL sPa +a++a++Ge+tdp lcl|NCBI__GCF_900176285.1:WP_084057448.1 347 AGATFVTPGCAACLGTHEGILAAGETCIASTNRNFPGRMGHTQSAVYLGSPAAVAAAALNGEVTDPS 413 *****************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (411 nodes) Target sequences: 1 (424 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: 10.66 // [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