Align 3-isopropylmalate dehydratase (EC 4.2.1.33); homoaconitate hydratase (EC 4.2.1.36) (characterized)
to candidate WP_048102793.1 MBAR_RS11505 3-isopropylmalate dehydratase large subunit
Query= BRENDA::P81291 (424 letters) >NCBI__GCF_000195895.1:WP_048102793.1 Length = 420 Score = 484 bits (1245), Expect = e-141 Identities = 245/424 (57%), Positives = 309/424 (72%), Gaps = 10/424 (2%) Query: 3 MTIVEKILAKASGKKEVSPGDIVMANIDVAMVHDITGPLTVN----TLKEYGIEKVWNPE 58 MT+ EKI +KASG V GD V+ANID+AM HDITGPL V +K+ +KVW+P Sbjct: 1 MTVSEKIFSKASGSP-VKAGDFVLANIDLAMTHDITGPLAVKGFYEIMKDKEEKKVWDPT 59 Query: 59 KIVILFDHQVPADSIKAAENHILMRKFVKEQGIKYFYDIREGVCHQVLPEKGHVAPGEVV 118 KIVI+FDHQVPADSI A NHI++RKF +EQGI YD+ EGVCHQVLPEKGHV PG+++ Sbjct: 60 KIVIVFDHQVPADSINATANHIMLRKFAEEQGILN-YDVYEGVCHQVLPEKGHVLPGDLI 118 Query: 119 VGADSHTCTHGAFGAFATGIGSTDMAHVFATGKLWFKVPETIYFNITGDLQPYVTSKDVI 178 VG+DSHTC +GA GAF+TGIGSTDMA VFATGKLWFKVPET F + G+L V SKD+I Sbjct: 119 VGSDSHTCAYGALGAFSTGIGSTDMAAVFATGKLWFKVPETFRFEVEGNLPERVYSKDLI 178 Query: 179 LSIIGEVGVDGATYKACQFGGETVKKMSIASRMTMTNMAIEMGGKTGIIEPDEKTIQYVK 238 L +IG+VGV+GA Y A +FGG T+ +SI RMTM+NMAIEMGGK GIIE DE T Y+K Sbjct: 179 LHLIGDVGVEGARYMAAEFGGSTIHSLSIPERMTMSNMAIEMGGKAGIIEADEVTANYLK 238 Query: 239 EAMKKHGTERPFEVIKGDEDAEFAEVYEIEADKIEPVFACPHNVDNVKQAREVAGKPIDQ 298 E + + + P+ K DEDA++ + + +EP ACPH+VDNVK EV G +DQ Sbjct: 239 ERIMYYEFD-PY--WKSDEDAKYVGIRHYDVSDLEPQVACPHHVDNVKPVTEVEGTKLDQ 295 Query: 299 VFIGSCTNGRLEDLRMAIKIIEKHGGIADDVRVVVTPASREEYLKALKEGIIEKFLKYGC 358 +F+GSCTNGR ED+++ I+ +A VR++V PASR EYLK LK G IEK + G Sbjct: 296 IFVGSCTNGRFEDIKIMADIMGDE-PVAKGVRLLVVPASRTEYLKLLKAGYIEKLMNAGA 354 Query: 359 VVTNPSCSACMGSLYGVLGPGEVCVSTSNRNFRGRQGSLEAEIYLASPITAAACAVKGEL 418 +V +P C CMG +G+LG GEV ++TSNRNF+GR+GS E+ +YL+SP TA A A+ GE+ Sbjct: 355 IVESPCCGPCMGGSFGLLGAGEVGLATSNRNFKGREGSPESFVYLSSPATAGASALTGEI 414 Query: 419 VDPR 422 DPR Sbjct: 415 TDPR 418 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: 611 Number of extensions: 36 Number of successful extensions: 6 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: 420 Length adjustment: 32 Effective length of query: 392 Effective length of database: 388 Effective search space: 152096 Effective search space used: 152096 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_048102793.1 MBAR_RS11505 (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.3413.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-169 548.2 0.0 5.9e-169 548.0 0.0 1.0 1 lcl|NCBI__GCF_000195895.1:WP_048102793.1 MBAR_RS11505 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195895.1:WP_048102793.1 MBAR_RS11505 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 548.0 0.0 5.9e-169 5.9e-169 1 410 [. 1 418 [. 1 419 [. 0.98 Alignments for each domain: == domain 1 score: 548.0 bits; conditional E-value: 5.9e-169 TIGR02086 1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelg.....akvekkekivlvfDhvv 64 +t+ eki+s+++G +vkaG+ v++++Dl+m+hD tgpl++k + e+ +kv++++kiv+vfDh+v lcl|NCBI__GCF_000195895.1:WP_048102793.1 1 MTVSEKIFSKASGSPVKAGDFVLANIDLAMTHDITGPLAVKGFYEIMkdkeeKKVWDPTKIVIVFDHQV 69 799**************************************99998878778899************** PP TIGR02086 65 PaptveaaelqkeirefakelgikvfdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGl 133 Pa +++a+ + ++r+fa e+gi ++dv eG+chqvl ekg++ pg+++vg+Dsht+ +Galgaf+tG+ lcl|NCBI__GCF_000195895.1:WP_048102793.1 70 PADSINATANHIMLRKFAEEQGILNYDVYEGVCHQVLPEKGHVLPGDLIVGSDSHTCAYGALGAFSTGI 138 ********************************************************************* PP TIGR02086 134 GatDvalalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsl 202 G+tD+a+++atGk+W+kvPe+++ e+eG+l e v++kD+il++++++g +ga y+a ef g++i++ls+ lcl|NCBI__GCF_000195895.1:WP_048102793.1 139 GSTDMAAVFATGKLWFKVPETFRFEVEGNLPERVYSKDLILHLIGDVGVEGARYMAAEFGGSTIHSLSI 207 ********************************************************************* PP TIGR02086 203 deRltlsnlaveagakaglvepdeetleylkkrrge...frilkadedakyeeeieidlseleplvavP 268 eR+t+sn+a+e+g+kag++e+de t +ylk+r + k+dedaky+ + d+s+lep+va+P lcl|NCBI__GCF_000195895.1:WP_048102793.1 208 PERMTMSNMAIEMGGKAGIIEADEVTANYLKERIMYyefDPYWKSDEDAKYVGIRHYDVSDLEPQVACP 276 *********************************99977545689************************* PP TIGR02086 269 hsvdnvkeveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGl 337 h+vdnvk+v+evegt++dq+f+GsCtnGR+ed+ki+a+i+ ++ v+k vrl+vvPasr+ y k l++G+ lcl|NCBI__GCF_000195895.1:WP_048102793.1 277 HHVDNVKPVTEVEGTKLDQIFVGSCTNGRFEDIKIMADIMGDEPVAKGVRLLVVPASRTEYLKLLKAGY 345 ********************************************************************* PP TIGR02086 338 ietlveaGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGei 406 ie+l++aGai+ +p CGPC+G +G l+ gev ++t+nRnfkGR Gsp++ +YL+sPa+a +sa++Gei lcl|NCBI__GCF_000195895.1:WP_048102793.1 346 IEKLMNAGAIVESPCCGPCMGGSFGLLGAGEVGLATSNRNFKGREGSPESFVYLSSPATAGASALTGEI 414 ********************************************************************* PP TIGR02086 407 tdpe 410 tdp+ lcl|NCBI__GCF_000195895.1:WP_048102793.1 415 TDPR 418 ***8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (411 nodes) Target sequences: 1 (420 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.56 // [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