Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_069663815.1 BCR25_RS11865 3-isopropylmalate dehydrogenase
Query= SwissProt::P12010 (366 letters) >NCBI__GCF_001730305.1:WP_069663815.1 Length = 346 Score = 378 bits (970), Expect = e-109 Identities = 194/356 (54%), Positives = 250/356 (70%), Gaps = 10/356 (2%) Query: 1 MKMKLAVLPGDGIGPEVMDAAIRVLKTVLDNDGHEAVFENALIGGAAIDEAGTPLPEETL 60 M ++ LPGDGIG E+MD+A+ +L ++ D + E GGA IDE G PLP+ETL Sbjct: 1 MSRRIVALPGDGIGTEIMDSALNILAEIMVQDNLDFDIERFAFGGAGIDEKGDPLPQETL 60 Query: 61 DICRRSDAILLGAVGGPKWDHNPASLRPEKGLLGLRKEMGLFANLRPVKAYATLLNASPL 120 + C ++DAILLGA+GGPKWD+ P RPE+GLLGLRK +GLFAN+RP+ +++ SPL Sbjct: 61 EACEQADAILLGAIGGPKWDNAPK--RPEQGLLGLRKALGLFANIRPISVPDAVVHLSPL 118 Query: 121 KRERVENVDLVIVRELTGGLYFGRPSERRGPGENEVVDTLAYTREEIERIIEKAFQLAQI 180 K E V VD V+VRELTGG+YFG + GE + D Y++ EI+RII KAF++AQ Sbjct: 119 KEENVRGVDFVVVRELTGGIYFGE----KQLGETQASDLCTYSKAEIQRIIRKAFEIAQT 174 Query: 181 RRKKLASVDKANVLESSRMWREIAEETAKKYPDVELSHMLVDSTSMQLIANPGQFDVIVT 240 R KK+ SVDKANVL +S++WR+ AEE AK++PD L + LVDS +M +I P QFDVIVT Sbjct: 175 RNKKVTSVDKANVLATSKLWRQTAEEVAKEFPDCTLENQLVDSAAMVMIQKPKQFDVIVT 234 Query: 241 ENMFGDILSDEASVITGSLGMLPSASLRSDRFGMYEPVHGSAPDIAGQGKANPLGTVLSA 300 EN+FGDILSDEASVI GSLGM+PSAS +YEP+HGSAPDIA Q ANP+ +LS Sbjct: 235 ENLFGDILSDEASVIPGSLGMMPSASHSETGPSLYEPIHGSAPDIANQNIANPMSMILSV 294 Query: 301 ALMLRYSFGLEKEAAAIEKAVDDVLQDGYCTGDLQVANGKVVSTIELTDRLIEKLN 356 A+MLR SFGLE+ A IE A D V+ G T DL G +T E T+ +I++L+ Sbjct: 295 AMMLRQSFGLEESAKKIEAACDCVMNQGILTTDL----GGKATTTEFTEAVIKELH 346 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: 368 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: 346 Length adjustment: 29 Effective length of query: 337 Effective length of database: 317 Effective search space: 106829 Effective search space used: 106829 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_069663815.1 BCR25_RS11865 (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.3447451.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-151 488.9 0.1 4.4e-151 488.8 0.1 1.0 1 NCBI__GCF_001730305.1:WP_069663815.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069663815.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 488.8 0.1 4.4e-151 4.4e-151 1 348 [. 4 344 .. 4 345 .. 0.98 Alignments for each domain: == domain 1 score: 488.8 bits; conditional E-value: 4.4e-151 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 +i+ LpGDgiG e++++al++L ++ + +l+++ e++ +GGa id++g+Plp+etl+ac++ada+Llga+GG NCBI__GCF_001730305.1:WP_069663815.1 4 RIVALPGDGIGTEIMDSALNILAEIMVQDNLDFDIERFAFGGAGIDEKGDPLPQETLEACEQADAILLGAIGG 76 699********************************************************************** PP TIGR00169 74 pkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkere 146 pkWdn +rPe+gLL lrk l+lfan+rP+ + +++++lsplkee v+gvD+vvvreLtgGiYfGe++ e NCBI__GCF_001730305.1:WP_069663815.1 77 PKWDNA--PKRPEQGLLGLRKALGLFANIRPISVPDAVVHLSPLKEENVRGVDFVVVRELTGGIYFGEKQLGE 147 ******..67*********************************************************987655 PP TIGR00169 147 eaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyi 219 ++a d +Y+k ei+ri+r+afe+a++r+kkvtsvDkanvL++s+lWr+t+ee+ake+Pd +le++++ NCBI__GCF_001730305.1:WP_069663815.1 148 -----TQASDLCTYSKAEIQRIIRKAFEIAQTRNKKVTSVDKANVLATSKLWRQTAEEVAKEFPDCTLENQLV 215 .....48****************************************************************** PP TIGR00169 220 DnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpi 292 D+aam ++++P+q+dv+vt+nlfGDilsDeasvi+GslG++Psas s++g l+ep+hgsapdia+++ianp+ NCBI__GCF_001730305.1:WP_069663815.1 216 DSAAMVMIQKPKQFDVIVTENLFGDILSDEASVIPGSLGMMPSASHSETGPSLYEPIHGSAPDIANQNIANPM 288 ************************************************************************* PP TIGR00169 293 aailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkeveee 348 ++ils+a++lr+s++lee+a++ieaa + v+++g+ t+dl+++att+ +t++v +e NCBI__GCF_001730305.1:WP_069663815.1 289 SMILSVAMMLRQSFGLEESAKKIEAACDCVMNQGILTTDLGGKATTTEFTEAVIKE 344 **************************************************999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (346 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 25.65 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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