Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate WP_013683216.1 ARCVE_RS02550 3-isopropylmalate dehydratase large subunit
Query= curated2:O28084 (416 letters) >NCBI__GCF_000194625.1:WP_013683216.1 Length = 415 Score = 667 bits (1722), Expect = 0.0 Identities = 318/416 (76%), Positives = 374/416 (89%), Gaps = 1/416 (0%) Query: 1 MGKTIAEKILSEKSKSDAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTHF 60 MGKTIAEKI SEKS SDAYAGDIVVA IDQIALQDGTAPLAIR +ME+G EVRAADRTHF Sbjct: 1 MGKTIAEKIFSEKSGSDAYAGDIVVARIDQIALQDGTAPLAIRSIMEMGLEVRAADRTHF 60 Query: 61 FVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADSH 120 FVDHAAPSPR+ELSNDQKFI EFA+KVGADFNPPGEGIIHQ+MVER++KPGDLAVGADSH Sbjct: 61 FVDHAAPSPRKELSNDQKFIREFAEKVGADFNPPGEGIIHQLMVERFIKPGDLAVGADSH 120 Query: 121 TCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIGD 180 TCTYG +GAF+TGMGSTD+AVA+ LGKNWFRVPE+FR++++G +PKGV+ KD+IL +IG Sbjct: 121 TCTYGALGAFATGMGSTDIAVAVVLGKNWFRVPETFRIEINGRMPKGVYPKDLILTVIGK 180 Query: 181 LGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGREG 240 LG DGATYKALEFHGE + M ++ RLT+ANMA+ECGAKAG+F+SD+ T+ +LAE+GRE Sbjct: 181 LGADGATYKALEFHGETIDGMYMDGRLTMANMAIECGAKAGLFKSDDITKAYLAEMGREN 240 Query: 241 DFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNGR 300 FRE+K DEDAEYEKEI+MD + + PVV+KPHNVDN+A ISEVEG V+QV++GTCTNGR Sbjct: 241 SFREIKPDEDAEYEKEIHMD-ADIEPVVAKPHNVDNIASISEVEGVNVDQVFVGTCTNGR 299 Query: 301 LSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPCV 360 LSD+E+ AR+LKGRKVK+G+RLIV PASR +YL+AL+KG ++ VEAGG++ PGC CV Sbjct: 300 LSDIEIVARMLKGRKVKKGLRLIVAPASRSIYLKALEKGYLKTIVEAGGLIAPPGCACCV 359 Query: 361 GIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPREFL 416 GIH GILAD EVC+STQNRNFKGRMGNPNAEI+LASPATAAA+A+KG IADPREFL Sbjct: 360 GIHMGILADNEVCVSTQNRNFKGRMGNPNAEIYLASPATAAATAIKGEIADPREFL 415 Lambda K H 0.318 0.136 0.391 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: 628 Number of extensions: 21 Number of successful extensions: 2 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: 416 Length of database: 415 Length adjustment: 31 Effective length of query: 385 Effective length of database: 384 Effective search space: 147840 Effective search space used: 147840 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_013683216.1 ARCVE_RS02550 (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.32282.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-173 563.6 0.7 1.3e-173 563.4 0.7 1.0 1 lcl|NCBI__GCF_000194625.1:WP_013683216.1 ARCVE_RS02550 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013683216.1 ARCVE_RS02550 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 563.4 0.7 1.3e-173 1.3e-173 1 411 [] 3 413 .. 3 413 .. 0.99 Alignments for each domain: == domain 1 score: 563.4 bits; conditional E-value: 1.3e-173 TIGR02086 1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelgakvekkekivlvfDhvvPaptv 69 kt+aeki+sek+G + aG+iv++++D+++++Dgt+pl+i+++ e+g +v+ ++ ++Dh++P+p++ lcl|NCBI__GCF_000194625.1:WP_013683216.1 3 KTIAEKIFSEKSGSDAYAGDIVVARIDQIALQDGTAPLAIRSIMEMGLEVRAADRTHFFVDHAAPSPRK 71 699****************************************************************** PP TIGR02086 70 eaaelqkeirefakelgikvfdvgeGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGatDv 138 e+++ qk irefa ++g geGi+hq++ve+ ++kpg++ vgaDsht+t+GalgafatG+G+tD+ lcl|NCBI__GCF_000194625.1:WP_013683216.1 72 ELSNDQKFIREFAEKVGADFNPPGEGIIHQLMVER-FIKPGDLAVGADSHTCTYGALGAFATGMGSTDI 139 ***********************************.********************************* PP TIGR02086 139 alalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealsldeRlt 207 a+a+++Gk+W++vPe++++e++G++ + v+ kD+il+++++lgadgatyka+ef+ge+i+ + +d+Rlt lcl|NCBI__GCF_000194625.1:WP_013683216.1 140 AVAVVLGKNWFRVPETFRIEINGRMPKGVYPKDLILTVIGKLGADGATYKALEFHGETIDGMYMDGRLT 208 ********************************************************************* PP TIGR02086 208 lsnlaveagakaglvepdeetleylkkrrge..frilkadedakyeeeieidlseleplvavPhsvdnv 274 ++n+a+e gakagl+++d+ t+ yl ++ +e fr++k+deda+ye+ei++d+ ++ep+va+Ph+vdn+ lcl|NCBI__GCF_000194625.1:WP_013683216.1 209 MANMAIECGAKAGLFKSDDITKAYLAEMGREnsFREIKPDEDAEYEKEIHMDA-DIEPVVAKPHNVDNI 276 **************************9998888*******************7.69************* PP TIGR02086 275 keveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyekaleeGlietlve 343 +++eveg+++dqvf+G+CtnGRl+d++i+a++l+gr+v+k rliv+Pasr++y kale+G+++t+ve lcl|NCBI__GCF_000194625.1:WP_013683216.1 277 ASISEVEGVNVDQVFVGTCTNGRLSDIEIVARMLKGRKVKKGLRLIVAPASRSIYLKALEKGYLKTIVE 345 ********************************************************************* PP TIGR02086 344 aGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavsaveGeitdpee 411 aG +i++pgC C+G h+G+lad+ev+vst+nRnfkGRmG+p+aeiYLasPa+aa++a++Gei+dp+e lcl|NCBI__GCF_000194625.1:WP_013683216.1 346 AGGLIAPPGCACCVGIHMGILADNEVCVSTQNRNFKGRMGNPNAEIYLASPATAAATAIKGEIADPRE 413 ******************************************************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (411 nodes) Target sequences: 1 (415 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.08 // [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