Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_092483013.1 BM299_RS08320 3-isopropylmalate dehydrogenase
Query= SwissProt::P12010 (366 letters) >NCBI__GCF_900115975.1:WP_092483013.1 Length = 356 Score = 404 bits (1037), Expect = e-117 Identities = 208/354 (58%), Positives = 266/354 (75%), Gaps = 3/354 (0%) Query: 4 KLAVLPGDGIGPEVMDAAIRVLKTVLDNDGHEAVFENALIGGAAIDEAGTPLPEETLDIC 63 K+ +LPGDGIGPEV A+RVL+ V G E + AL GG A D+ GTPLPEETL +C Sbjct: 3 KITLLPGDGIGPEVTAGAVRVLQAVQKCTGVEITMQEALFGGCAYDKTGTPLPEETLRLC 62 Query: 64 RRSDAILLGAVGGPKWDHNPASLRPEKG-LLGLRKEMGLFANLRPVKAYATLLNASPLKR 122 DA+LLGAVGGP+WD+ P LRPE+G LL LRKE+G+FANLRP + +L +AS LKR Sbjct: 63 LEGDAVLLGAVGGPRWDNLPVHLRPERGALLPLRKELGVFANLRPSLIFPSLADASTLKR 122 Query: 123 ERVENVDLVIVRELTGGLYFGRPSERRGP-GENEVVDTLAYTREEIERIIEKAFQLAQIR 181 E V+ +DL++VRELTGG+YFG+ P G VV+TL YT EIER+ AF+LA+ R Sbjct: 123 EVVDGLDLMVVRELTGGIYFGKKQREDLPEGGYRVVETLEYTTGEIERVARVAFELARKR 182 Query: 182 RKKLASVDKANVLESSRMWREIAEETAKKYPDVELSHMLVDSTSMQLIANPGQFDVIVTE 241 R KL SVDKANVLESSR+WRE+ A +YPDVEL+HMLVD+ +MQL+ NP QFDV++TE Sbjct: 183 RCKLTSVDKANVLESSRLWREVVSGLAAEYPDVELNHMLVDNCAMQLVRNPKQFDVLLTE 242 Query: 242 NMFGDILSDEASVITGSLGMLPSASLRSDRFGMYEPVHGSAPDIAGQGKANPLGTVLSAA 301 NMFGDILSD+AS +TGS+GMLPSASL + G++EP+HGSAPDIAG+ ANP+ ++LS A Sbjct: 243 NMFGDILSDQASQLTGSIGMLPSASL-GGKVGLFEPIHGSAPDIAGKDIANPIASILSVA 301 Query: 302 LMLRYSFGLEKEAAAIEKAVDDVLQDGYCTGDLQVANGKVVSTIELTDRLIEKL 355 +MLRYSF LE+EAA +E+AV VL++GY T D+ + VST E+ + + K+ Sbjct: 302 MMLRYSFNLEEEAALVERAVSAVLEEGYRTTDIMQPGMRRVSTGEMAELIAGKI 355 Lambda K H 0.316 0.135 0.379 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: 414 Number of extensions: 15 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: 366 Length of database: 356 Length adjustment: 29 Effective length of query: 337 Effective length of database: 327 Effective search space: 110199 Effective search space used: 110199 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_092483013.1 BM299_RS08320 (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.9941.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-158 513.8 0.0 1.2e-158 513.6 0.0 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092483013.1 BM299_RS08320 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092483013.1 BM299_RS08320 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 513.6 0.0 1.2e-158 1.2e-158 1 348 [. 3 350 .. 3 351 .. 0.99 Alignments for each domain: == domain 1 score: 513.6 bits; conditional E-value: 1.2e-158 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 ki++LpGDgiGpev+a a++vL+av++ ++++++++eal+GG a d+tg+Plpeetl+ c e davLlg lcl|NCBI__GCF_900115975.1:WP_092483013.1 3 KITLLPGDGIGPEVTAGAVRVLQAVQKCTGVEITMQEALFGGCAYDKTGTPLPEETLRLCLEGDAVLLG 71 79******************************************************************* PP TIGR00169 70 avGGpkWdnlprdvrPek.gLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGi 137 avGGp+Wdnlp + rPe+ +LL+lrkel++fanLrP+ +f+sL ++s+lk+e+v+g+Dl+vvreLtgGi lcl|NCBI__GCF_900115975.1:WP_092483013.1 72 AVGGPRWDNLPVHLRPERgALLPLRKELGVFANLRPSLIFPSLADASTLKREVVDGLDLMVVRELTGGI 140 ******************88************************************************* PP TIGR00169 138 YfGepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206 YfG+++ ++ e + ++t +Yt+ eier+arvafelarkrr k+tsvDkanvLessrlWr++v+ +a lcl|NCBI__GCF_900115975.1:WP_092483013.1 141 YFGKKQREDLPEGGYRVVETLEYTTGEIERVARVAFELARKRRCKLTSVDKANVLESSRLWREVVSGLA 209 *****99999888999***************************************************** PP TIGR00169 207 keyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275 eyPdvel+h+++Dn+amqLv++P+q+dv++t+n+fGDilsD+as +tGs+G+LPsasl+ +++lfep lcl|NCBI__GCF_900115975.1:WP_092483013.1 210 AEYPDVELNHMLVDNCAMQLVRNPKQFDVLLTENMFGDILSDQASQLTGSIGMLPSASLG-GKVGLFEP 277 ************************************************************.6679**** PP TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344 +hgsapdiagk+ianpia ils+a++lrys+nlee+a+ +e+av+ vleeg+rt+d+++ + +vst e lcl|NCBI__GCF_900115975.1:WP_092483013.1 278 IHGSAPDIAGKDIANPIASILSVAMMLRYSFNLEEEAALVERAVSAVLEEGYRTTDIMQPGMRRVSTGE 346 ********************************************************************* PP TIGR00169 345 veee 348 + e lcl|NCBI__GCF_900115975.1:WP_092483013.1 347 MAEL 350 9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (356 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: 7.28 // [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