Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_042204148.1 NITSA_RS03120 3-isopropylmalate dehydrogenase
Query= BRENDA::P93832 (405 letters) >NCBI__GCF_000186245.1:WP_042204148.1 Length = 355 Score = 417 bits (1073), Expect = e-121 Identities = 219/351 (62%), Positives = 263/351 (74%), Gaps = 7/351 (1%) Query: 41 KRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETI 100 + Y I ++ GDGIGPE+V A VL S+E + F++ E +GGAA+D GVPLPEETI Sbjct: 2 RSYKIGVIKGDGIGPEIVDEAIKVLDAVASVEQINFDYEEFLLGGAAIDETGVPLPEETI 61 Query: 101 SAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTL 160 K+ DAVL GAIGG KWD E+HLRPE GLL +R A+ FANLRPATV +L++ASTL Sbjct: 62 QGVKKVDAVLFGAIGGPKWDTLERHLRPESGLLGLRKAMGTFANLRPATVYDELINASTL 121 Query: 161 KREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETA 220 K EV +GVD+MVVRELTGGIYFG+PR E GEE +NT VY E++RIA+VAFE A Sbjct: 122 KPEVVKGVDIMVVRELTGGIYFGQPR-----EYGEEKAYNTMVYTRPEVERIAKVAFEIA 176 Query: 221 RKRRGKLCSVDKANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTI 280 KR ++CSVDKANVLE S WR V + +YP+VELSHMYVDNAAMQL+RDPKQFD I Sbjct: 177 MKRDKRVCSVDKANVLEVSQFWRDIVEEVHRDYPEVELSHMYVDNAAMQLIRDPKQFDVI 236 Query: 281 VTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATIL 340 +T NIFGDILSD ASM++GSIG+LPSAS + G GLFEPIHGSAPDIAGQ ANP+ATI Sbjct: 237 LTGNIFGDILSDAASMLSGSIGLLPSASTGE-GVGLFEPIHGSAPDIAGQGIANPIATIA 295 Query: 341 SAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTK-LVGCKEMG 390 SA+M+L+Y LGEE AA RI+ A+ AL G+RT DI + K +V EMG Sbjct: 296 SASMMLRYALGEESAADRIDTAIKKALAEGYRTQDIAAFDAKEVVSTSEMG 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: 431 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: 355 Length adjustment: 30 Effective length of query: 375 Effective length of database: 325 Effective search space: 121875 Effective search space used: 121875 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_042204148.1 NITSA_RS03120 (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.668131.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-163 529.8 0.1 1.7e-163 529.6 0.1 1.0 1 NCBI__GCF_000186245.1:WP_042204148.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000186245.1:WP_042204148.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 529.6 0.1 1.7e-163 1.7e-163 1 347 [. 5 347 .. 5 349 .. 0.97 Alignments for each domain: == domain 1 score: 529.6 bits; conditional E-value: 1.7e-163 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 ki v++GDgiGpe+v+ea+kvL+av+ +++++++ee+l+GGaaid+tg Plpeet++++k++davL+ga+GG NCBI__GCF_000186245.1:WP_042204148.1 5 KIGVIKGDGIGPEIVDEAIKVLDAVASVEQINFDYEEFLLGGAAIDETGVPLPEETIQGVKKVDAVLFGAIGG 77 799********************************************************************** PP TIGR00169 74 pkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepkere 146 pkWd+l r+ rPe+gLL lrk ++ fanLrPa+++++L+++s+lk+e+vkgvD++vvreLtgGiYfG+p+e NCBI__GCF_000186245.1:WP_042204148.1 78 PKWDTLERHLRPESGLLGLRKAMGTFANLRPATVYDELINASTLKPEVVKGVDIMVVRELTGGIYFGQPREYG 150 **********************************************************************988 PP TIGR00169 147 eaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyi 219 e +ka++t++Yt++e+eria+vafe+a+kr k+v+svDkanvLe+s++Wr++vee++++yP+vel+h+y+ NCBI__GCF_000186245.1:WP_042204148.1 151 E----EKAYNTMVYTRPEVERIAKVAFEIAMKRDKRVCSVDKANVLEVSQFWRDIVEEVHRDYPEVELSHMYV 219 7....89****************************************************************** PP TIGR00169 220 DnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpi 292 DnaamqL+++P+q+dv++t+n+fGDilsD as+++Gs+GlLPsas + +g++lfep+hgsapdiag+gianpi NCBI__GCF_000186245.1:WP_042204148.1 220 DNAAMQLIRDPKQFDVILTGNIFGDILSDAASMLSGSIGLLPSASTG-EGVGLFEPIHGSAPDIAGQGIANPI 291 *********************************************99.99*********************** PP TIGR00169 293 aailsaalllryslnleeaaeaieaavkkvleegkrtedlas.eattavstkevee 347 a+i sa+++lry+l+ e aa++i++a+kk+l+eg+rt+d+a +a + vst+e+++ NCBI__GCF_000186245.1:WP_042204148.1 292 ATIASASMMLRYALGEESAADRIDTAIKKALAEGYRTQDIAAfDAKEVVSTSEMGS 347 ****************************************9724555677888765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (355 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.92 // [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