Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_084275692.1 B8779_RS06295 3-isopropylmalate dehydrogenase
Query= BRENDA::P93832 (405 letters) >NCBI__GCF_900176045.1:WP_084275692.1 Length = 356 Score = 409 bits (1050), Expect = e-119 Identities = 215/351 (61%), Positives = 258/351 (73%), Gaps = 7/351 (1%) Query: 41 KRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETI 100 KRYT+ L+ GDGIGPE++ A VL EG E ++E +GGAA+D+ G P+PEETI Sbjct: 2 KRYTVALIKGDGIGPEIIDEAVKVLDAVSVKEGFEITYKEALLGGAAIDVTGEPIPEETI 61 Query: 101 SAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTL 160 AK +DAVL GAIGG +WD+ + RPE GLL++R AL+VFANLRP TV +LV+ASTL Sbjct: 62 EIAKSADAVLFGAIGGPQWDDLPRDKRPETGLLKLRKALEVFANLRPVTVYDELVNASTL 121 Query: 161 KREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETA 220 K EV +G DLMVVREL GGIYFG+PR + + +NT VY E+ RIA+V FE A Sbjct: 122 KPEVIQGTDLMVVRELIGGIYFGQPRAYEGDR-----AYNTMVYTKQEVYRIAKVGFEIA 176 Query: 221 RKRRGKLCSVDKANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTI 280 KR KL SVDKANVLE S LWR V +A EYP+V + HMYVDNAAMQLVRDPKQFD I Sbjct: 177 MKRNKKLVSVDKANVLEVSQLWRDTVNEVAKEYPEVSVEHMYVDNAAMQLVRDPKQFDVI 236 Query: 281 VTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATIL 340 +T NIFGDILSDEASM++GSIG+LPSAS+ + GL+EPIHGSAPDIAGQ ANP+ATI Sbjct: 237 LTGNIFGDILSDEASMLSGSIGLLPSASIGEK-YGLYEPIHGSAPDIAGQGIANPIATIA 295 Query: 341 SAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTK-LVGCKEMG 390 SAAM+L+Y GEE AAKRIEDA+ L G+RT D+ S K +V EMG Sbjct: 296 SAAMMLRYQFGEESAAKRIEDAIKRVLKEGYRTKDLSSFDAKEVVTTSEMG 346 Lambda K H 0.316 0.134 0.374 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: 418 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: 405 Length of database: 356 Length adjustment: 30 Effective length of query: 375 Effective length of database: 326 Effective search space: 122250 Effective search space used: 122250 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: 50 (23.9 bits)
Align candidate WP_084275692.1 B8779_RS06295 (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.2083360.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-164 533.0 0.2 1.8e-164 532.8 0.2 1.0 1 NCBI__GCF_900176045.1:WP_084275692.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900176045.1:WP_084275692.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 532.8 0.2 1.8e-164 1.8e-164 2 345 .. 6 345 .. 5 349 .. 0.97 Alignments for each domain: == domain 1 score: 532.8 bits; conditional E-value: 1.8e-164 TIGR00169 2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGp 74 +a+++GDgiGpe+++ea+kvL+av+ +++++++++eal+GGaaid tgeP+peet++ +k+adavL+ga+GGp NCBI__GCF_900176045.1:WP_084275692.1 6 VALIKGDGIGPEIIDEAVKVLDAVSVKEGFEITYKEALLGGAAIDVTGEPIPEETIEIAKSADAVLFGAIGGP 78 899********************************************************************** PP TIGR00169 75 kWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkeree 147 +Wd+lprd+rPe+gLLklrk l++fanLrP++++++L+++s+lk+e+++g+Dl+vvreL+gGiYfG+p+ e+ NCBI__GCF_900176045.1:WP_084275692.1 79 QWDDLPRDKRPETGLLKLRKALEVFANLRPVTVYDELVNASTLKPEVIQGTDLMVVRELIGGIYFGQPRAYEG 151 ************************************************************************9 PP TIGR00169 148 aeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiD 220 ++a++t++Ytk+e+ ria+v+fe+a+kr+kk++svDkanvLe+s+lWr+tv+e+akeyP+v++eh+y+D NCBI__GCF_900176045.1:WP_084275692.1 152 ----DRAYNTMVYTKQEVYRIAKVGFEIAMKRNKKLVSVDKANVLEVSQLWRDTVNEVAKEYPEVSVEHMYVD 220 ....69******************************************************************* PP TIGR00169 221 naamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpia 293 naamqLv++P+q+dv++t+n+fGDilsDeas+++Gs+GlLPsas++ ++++l+ep+hgsapdiag+gianpia NCBI__GCF_900176045.1:WP_084275692.1 221 NAAMQLVRDPKQFDVILTGNIFGDILSDEASMLSGSIGLLPSASIG-EKYGLYEPIHGSAPDIAGQGIANPIA 292 **********************************************.8899********************** PP TIGR00169 294 ailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavs.tkev 345 +i saa++lry+++ e aa++ie+a+k+vl+eg+rt+dl s ++++v+ t+e+ NCBI__GCF_900176045.1:WP_084275692.1 293 TIASAAMMLRYQFGEESAAKRIEDAIKRVLKEGYRTKDLSSFDAKEVVtTSEM 345 ***************************************99777666504555 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 15.77 // [ok]
This GapMind analysis is from Jul 25 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