Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_057509305.1 ABB28_RS14510 3-isopropylmalate dehydrogenase
Query= SwissProt::P12010 (366 letters) >NCBI__GCF_001431535.1:WP_057509305.1 Length = 354 Score = 374 bits (961), Expect = e-108 Identities = 198/357 (55%), Positives = 250/357 (70%), Gaps = 7/357 (1%) Query: 1 MKMKLAVLPGDGIGPEVMDAAIRVLKTVLDNDGHEAVFENALIGGAAIDEAGTPLPEETL 60 M ++ VLPGDGIGPEV AA+ VL+ V H F IGG AID G PLP TL Sbjct: 1 MHAEIVVLPGDGIGPEVAAAAVAVLEAVATRFNHTFNFNEHDIGGIAIDRHGEPLPASTL 60 Query: 61 DICRRSDAILLGAVGGPKWDHNPASLRPEKGLLGLRKEMGLFANLRPVKAYATLLNASPL 120 D CR +DAILLGAVGGPKW A +RPE+GLL +R+ +GL+ANLRPV+ + L ASP+ Sbjct: 61 DACRAADAILLGAVGGPKWSDPNAKVRPEQGLLAIRRALGLYANLRPVRTHEAALGASPI 120 Query: 121 KRERVENVDLVIVRELTGGLYFGRPSERRGPGENEVVDTLAYTREEIERIIEKAFQLAQI 180 K E + VD V+VRELTGG+YFG + + D +Y+ EEIER++ AF+LA+ Sbjct: 121 KAELLRGVDFVVVRELTGGIYFGEKTRT----ADAASDLCSYSVEEIERVLRSAFELARQ 176 Query: 181 RRKKLASVDKANVLESSRMWREIAEETAKK-YPDVELSHMLVDSTSMQLIANPGQFDVIV 239 RR K+ SVDKANVLE+SR+WR++A + +PDV L H LVDS +M L+A P ++DVIV Sbjct: 177 RRGKVTSVDKANVLETSRLWRDVATRLGRDVFPDVALEHQLVDSMAMHLLAKPREYDVIV 236 Query: 240 TENMFGDILSDEASVITGSLGMLPSASL-RSDRFGMYEPVHGSAPDIAGQGKANPLGTVL 298 TENMFGDIL+DEAS++ GSLG+LPSASL + G+YEP+HGSAPDIAG+G ANP T+ Sbjct: 237 TENMFGDILTDEASMLAGSLGLLPSASLGQPGAVGIYEPIHGSAPDIAGKGIANPYATIF 296 Query: 299 SAALMLRYSFGLEKEAAAIEKAVDDVLQDGYCTGDLQVANGKVVSTIELTDRLIEKL 355 SAA++LR+S GLE EAAA+E AV L G T DL A G VST E T ++E+L Sbjct: 297 SAAMLLRHSLGLEAEAAAVEAAVHAALDAGVFTADLAAA-GAAVSTAEATAAVLERL 352 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: 397 Number of extensions: 18 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: 354 Length adjustment: 29 Effective length of query: 337 Effective length of database: 325 Effective search space: 109525 Effective search space used: 109525 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_057509305.1 ABB28_RS14510 (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.28802.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-149 482.4 0.1 4.6e-149 482.1 0.1 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509305.1 ABB28_RS14510 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057509305.1 ABB28_RS14510 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 482.1 0.1 4.6e-149 4.6e-149 2 346 .. 5 345 .. 4 349 .. 0.97 Alignments for each domain: == domain 1 score: 482.1 bits; conditional E-value: 4.6e-149 TIGR00169 2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 i+vLpGDgiGpev a+a++vL+av+ rf++ ++f+e++iGG aid++gePlp+ tl+ac++ada+Llga lcl|NCBI__GCF_001431535.1:WP_057509305.1 5 IVVLPGDGIGPEVAAAAVAVLEAVATRFNHTFNFNEHDIGGIAIDRHGEPLPASTLDACRAADAILLGA 73 9******************************************************************** PP TIGR00169 71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYf 139 vGGpkW + ++vrPe+gLL++r+ l+l+anLrP++ +++ + +sp+k+e+ +gvD+vvvreLtgGiYf lcl|NCBI__GCF_001431535.1:WP_057509305.1 74 VGGPKWSDPNAKVRPEQGLLAIRRALGLYANLRPVRTHEAALGASPIKAELLRGVDFVVVRELTGGIYF 142 ********************************************************************* PP TIGR00169 140 GepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak. 207 Ge++ + + a d +Y++eeier+ r afelar+rr kvtsvDkanvLe+srlWr++++ + + lcl|NCBI__GCF_001431535.1:WP_057509305.1 143 GEKTRTAD-----AASDLCSYSVEEIERVLRSAFELARQRRGKVTSVDKANVLETSRLWRDVATRLGRd 206 **998887.....79***************************************************996 PP TIGR00169 208 eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss.kglalfep 275 +Pdv+leh+++D++am+L+ +P+++dv+vt+n+fGDil Deas+++GslGlLPsasl++ ++++ep lcl|NCBI__GCF_001431535.1:WP_057509305.1 207 VFPDVALEHQLVDSMAMHLLAKPREYDVIVTENMFGDILTDEASMLAGSLGLLPSASLGQpGAVGIYEP 275 7**********************************************************955678**** PP TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344 +hgsapdiagkgianp a+i saa+llr+sl+le +a+a+eaav+ +l+ g t+dla + +avst+e lcl|NCBI__GCF_001431535.1:WP_057509305.1 276 IHGSAPDIAGKGIANPYATIFSAAMLLRHSLGLEAEAAAVEAAVHAALDAGVFTADLAAAG-AAVSTAE 343 *********************************************************9988.7777777 PP TIGR00169 345 ve 346 ++ lcl|NCBI__GCF_001431535.1:WP_057509305.1 344 AT 345 65 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (354 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: 11.94 // [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