Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_029933935.1 N746_RS0103275 3-isopropylmalate dehydrogenase
Query= SwissProt::Q56268 (358 letters) >NCBI__GCF_000711195.1:WP_029933935.1 Length = 358 Score = 436 bits (1122), Expect = e-127 Identities = 224/355 (63%), Positives = 274/355 (77%), Gaps = 2/355 (0%) Query: 2 KKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQL 61 KK+ + GDGIGPEIVA A +VLDA+ L + GL+GGAA DAS PL ++Q+ Sbjct: 3 KKVLLLPGDGIGPEIVAEAVKVLDALKANHGLDIEMVSGLIGGAAYDASGHPLTDETMQM 62 Query: 62 AMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRP 121 A DA++LGAVGG +W++ + RPE+GLL LR GL L+ANLRPA ++PQL DAS L+P Sbjct: 63 ARDVDAILLGAVGGYKWESLDISVRPEKGLLGLRSGLSLFANLRPAFLYPQLADASTLKP 122 Query: 122 ELVRDVDILVVRELTGDIYFGQPRGLEVID-GKRRGFNTMVYDEDEIRRIAHVAFRAAQG 180 E+V +DIL+VRELTG IYFGQPRG+ ++ G+R+G+NT VY E EI RI HVAF+AA Sbjct: 123 EVVSGLDILIVRELTGGIYFGQPRGIRTLENGERQGYNTYVYSESEIVRIGHVAFQAAMK 182 Query: 181 RRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLT 240 R K++CSVDKANVLE T LWREV+T++A+ YP+V L+HMYVDNAAMQL+R P QFDV++T Sbjct: 183 RNKKVCSVDKANVLEVTELWREVMTDLAKQYPEVELTHMYVDNAAMQLVRNPKQFDVVVT 242 Query: 241 GNMFGDILSDEASQLTGSIGMLPSASL-GEGRAMYEPIHGSAPDIAGQDKANPLATILSV 299 GNMFGDILSDEAS LTGSIGMLPSASL + MYEP HGSAPDIAGQ+ ANPLATILS Sbjct: 243 GNMFGDILSDEASMLTGSIGMLPSASLDANNKGMYEPSHGSAPDIAGQNLANPLATILSA 302 Query: 300 AMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354 AMMLR+SL E A ++E AV +VLDQGLRT DI + G + T MG+AVV AL Sbjct: 303 AMMLRYSLGREDLALKIEQAVSKVLDQGLRTGDIYSEGMKKVSTSEMGSAVVKAL 357 Lambda K H 0.320 0.137 0.396 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: 424 Number of extensions: 10 Number of successful extensions: 3 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: 358 Length of database: 358 Length adjustment: 29 Effective length of query: 329 Effective length of database: 329 Effective search space: 108241 Effective search space used: 108241 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: 49 (23.5 bits)
Align candidate WP_029933935.1 N746_RS0103275 (3-isopropylmalate dehydrogenase)
to HMM TIGR00169 (leuB: 3-isopropylmalate dehydrogenase (EC 1.1.1.85))
# 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/TIGR00169.hmm # target sequence database: /tmp/gapView.21843.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00169 [M=349] Accession: TIGR00169 Description: leuB: 3-isopropylmalate dehydrogenase 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-157 510.5 0.1 1.3e-157 510.3 0.1 1.0 1 lcl|NCBI__GCF_000711195.1:WP_029933935.1 N746_RS0103275 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711195.1:WP_029933935.1 N746_RS0103275 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 510.3 0.1 1.3e-157 1.3e-157 1 347 [. 4 351 .. 4 353 .. 0.99 Alignments for each domain: == domain 1 score: 510.3 bits; conditional E-value: 1.3e-157 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 k+ +LpGDgiGpe+vaea+kvL+a++ +++l++e+ + liGGaa da g+Pl++et++ ++++da+Llg lcl|NCBI__GCF_000711195.1:WP_029933935.1 4 KVLLLPGDGIGPEIVAEAVKVLDALKANHGLDIEMVSGLIGGAAYDASGHPLTDETMQMARDVDAILLG 72 6899***************************************************************** PP TIGR00169 70 avGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138 avGG+kW++l +vrPekgLL lr l lfanLrPa l+++L ++s+lk+e+v+g+D+++vreLtgGiY lcl|NCBI__GCF_000711195.1:WP_029933935.1 73 AVGGYKWESLDISVRPEKGLLGLRSGLSLFANLRPAFLYPQLADASTLKPEVVSGLDILIVRELTGGIY 141 ********************************************************************* PP TIGR00169 139 fGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206 fG+p++++ e+ e+++++t +Y+++ei ri +vaf++a+kr+kkv+svDkanvLe+++lWr++++++a lcl|NCBI__GCF_000711195.1:WP_029933935.1 142 FGQPRGIRTLENgERQGYNTYVYSESEIVRIGHVAFQAAMKRNKKVCSVDKANVLEVTELWREVMTDLA 210 ********99999******************************************************** PP TIGR00169 207 keyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275 k+yP+vel h+y+DnaamqLv++P+q+dvvvt+n+fGDilsDeas++tGs+G+LPsasl + ++++ep lcl|NCBI__GCF_000711195.1:WP_029933935.1 211 KQYPEVELTHMYVDNAAMQLVRNPKQFDVVVTGNMFGDILSDEASMLTGSIGMLPSASLDANNKGMYEP 279 ********************************************************************* PP TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344 hgsapdiag+++anp+a+ilsaa++lrysl+ e+ a +ie+av+kvl++g rt d++se+ ++vst+e lcl|NCBI__GCF_000711195.1:WP_029933935.1 280 SHGSAPDIAGQNLANPLATILSAAMMLRYSLGREDLALKIEQAVSKVLDQGLRTGDIYSEGMKKVSTSE 348 ********************************************************************* PP TIGR00169 345 vee 347 +++ lcl|NCBI__GCF_000711195.1:WP_029933935.1 349 MGS 351 986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (358 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: 00:00:00.01 # Mc/sec: 6.75 // [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