Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_066923041.1 ACG33_RS08110 3-isopropylmalate dehydrogenase
Query= SwissProt::P12010 (366 letters) >NCBI__GCF_001579945.1:WP_066923041.1 Length = 351 Score = 363 bits (932), Expect = e-105 Identities = 188/356 (52%), Positives = 246/356 (69%), Gaps = 6/356 (1%) Query: 1 MKMKLAVLPGDGIGPEVMDAAIRVLKTVLDNDGHEAVFENALIGGAAIDEAGTPLPEETL 60 M+ + VLPGDG+GPEV A+RVL+ V GH FE+ IGGAAID G+ LP T Sbjct: 1 MQATIVVLPGDGVGPEVTHEAVRVLEAVAARRGHSFDFESHPIGGAAIDACGSALPPGTT 60 Query: 61 DICRRSDAILLGAVGGPKWDHNPASLRPEKGLLGLRKEMGLFANLRPVKAYATLLNASPL 120 C+R+ A+LLGAVGGPKW A +RPE+GLL LRK + LFANLRPV + LL+ SPL Sbjct: 61 AACQRAHAVLLGAVGGPKWSDPAAPVRPEQGLLALRKALNLFANLRPVTLHPALLDVSPL 120 Query: 121 KRERVENVDLVIVRELTGGLYFGRPSERRGPGENEVVDTLAYTREEIERIIEKAFQLAQI 180 K + ++ D+++VRELTGG+YFG D Y+ EEIER+ A LA+ Sbjct: 121 KADILQGTDIMVVRELTGGIYFGEKQRTA----TFASDLCTYSVEEIERVTRVAGTLARS 176 Query: 181 RRKKLASVDKANVLESSRMWREIAEETAK-KYPDVELSHMLVDSTSMQLIANPGQFDVIV 239 RR+ + SVDKANVLE+SR+WR E K ++PDV+ HMLVD+ +M LI P FDVI+ Sbjct: 177 RRRSIVSVDKANVLETSRLWRSTVESLLKTEFPDVKFEHMLVDAAAMHLIRRPSSFDVIL 236 Query: 240 TENMFGDILSDEASVITGSLGMLPSASLRSDRFGMYEPVHGSAPDIAGQGKANPLGTVLS 299 TENMFGDIL+DEAS++ GSLG+LPSASL S G+YEP+HGSAPDIAGQG ANP GT+LS Sbjct: 237 TENMFGDILTDEASMLAGSLGLLPSASLGSGTQGLYEPIHGSAPDIAGQGVANPYGTILS 296 Query: 300 AALMLRYSFGLEKEAAAIEKAVDDVLQDGYCTGDLQVANGKVVSTIELTDRLIEKL 355 AA++LR+S GL +EAA +EKAV + + G T D+ +GK +T + +++++ Sbjct: 297 AAMLLRHSLGLHEEAALVEKAVAEAIVAGVRTADIG-GSGKAATTAQAGSAVVDRI 351 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: 393 Number of extensions: 12 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: 366 Length of database: 351 Length adjustment: 29 Effective length of query: 337 Effective length of database: 322 Effective search space: 108514 Effective search space used: 108514 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_066923041.1 ACG33_RS08110 (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.6970.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-150 487.6 0.0 1.2e-150 487.3 0.0 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066923041.1 ACG33_RS08110 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066923041.1 ACG33_RS08110 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 487.3 0.0 1.2e-150 1.2e-150 2 345 .. 5 343 .. 4 349 .. 0.97 Alignments for each domain: == domain 1 score: 487.3 bits; conditional E-value: 1.2e-150 TIGR00169 2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 i+vLpGDg+Gpev+ ea++vL+av+ r +++++fe++ iGGaaida+g+ lp t +ac++a avLlga lcl|NCBI__GCF_001579945.1:WP_066923041.1 5 IVVLPGDGVGPEVTHEAVRVLEAVAARRGHSFDFESHPIGGAAIDACGSALPPGTTAACQRAHAVLLGA 73 9******************************************************************** PP TIGR00169 71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYf 139 vGGpkW + + vrPe+gLL+lrk l+lfanLrP++l+++L+++splk++i +g+D++vvreLtgGiYf lcl|NCBI__GCF_001579945.1:WP_066923041.1 74 VGGPKWSDPAAPVRPEQGLLALRKALNLFANLRPVTLHPALLDVSPLKADILQGTDIMVVRELTGGIYF 142 ********************************************************************* PP TIGR00169 140 GepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak. 207 Ge++ + a d +Y++eeier++rva +lar rr+ ++svDkanvLe+srlWr tve + k lcl|NCBI__GCF_001579945.1:WP_066923041.1 143 GEKQRTAT-----FASDLCTYSVEEIERVTRVAGTLARSRRRSIVSVDKANVLETSRLWRSTVESLLKt 206 *9987776.....8***************************************************9999 PP TIGR00169 208 eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepv 276 e+Pdv++eh+++D+aam+L+++P+++dv++t+n+fGDil Deas+++GslGlLPsasl+s +++l+ep+ lcl|NCBI__GCF_001579945.1:WP_066923041.1 207 EFPDVKFEHMLVDAAAMHLIRRPSSFDVILTENMFGDILTDEASMLAGSLGLLPSASLGSGTQGLYEPI 275 ********************************************************************* PP TIGR00169 277 hgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkev 345 hgsapdiag+g+anp ++ilsaa+llr+sl+l+e+a+ +e+av+++ g rt+d+++++ +a++t+++ lcl|NCBI__GCF_001579945.1:WP_066923041.1 276 HGSAPDIAGQGVANPYGTILSAAMLLRHSLGLHEEAALVEKAVAEAIVAGVRTADIGGSG-KAATTAQA 343 *********************************************************998.55555554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (351 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: 7.16 // [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