Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_010526307.1 GQW_RS0101545 3-isopropylmalate dehydrogenase
Query= BRENDA::P54354 (353 letters) >NCBI__GCF_000220155.1:WP_010526307.1 Length = 355 Score = 439 bits (1128), Expect = e-128 Identities = 227/354 (64%), Positives = 272/354 (76%), Gaps = 6/354 (1%) Query: 1 MDFKIAVLAGDGIGPEISVQGVEVMSAVCEKFGHKVNYEYAICGADAIDKVGDPFPEETY 60 M IAVL GDGIGPEI Q + + AV +K GH+ NY A GA AID+ GDP+PEET+ Sbjct: 1 MKLNIAVLPGDGIGPEIVEQAKKSLDAVLKKKGHEANYTEAPVGAVAIDQTGDPYPEETH 60 Query: 61 RVCKNADAVLFSAVGDPKFDNDPTAKVRPEQGLLAMRKKLGLFANIRPVQTFKCLVHKSP 120 ++C NADAVLF A+GDPK+DNDP AKVRPEQGLLAMRKKLGL+ANIRPV TF L+HKSP Sbjct: 61 QICMNADAVLFGAIGDPKYDNDPKAKVRPEQGLLAMRKKLGLYANIRPVTTFPSLIHKSP 120 Query: 121 LRAELVEGADFLCIRELTGGMYFGE---KYQDNDKAYDTNMYTRPEIERILKVGFEYAMK 177 LR++LV+GADF+ IRELTGG+YFG + +D AYDTN+YT EIERI ++ F++AMK Sbjct: 121 LRSDLVDGADFVAIRELTGGIYFGRPQGRSEDGRTAYDTNVYTVEEIERITRLAFDFAMK 180 Query: 178 RRKHLTVVDKANVLASSRLWRQIAQEMAPQYPEVTTDYMFVDNAAMKMIQEPKFFDVMVT 237 RRK LTVVDKANVLA+SRLWR+ Q +AP + EV +YMFVDNAAM++IQ PK FDVM+T Sbjct: 181 RRKKLTVVDKANVLATSRLWRETVQAIAPDFLEVEVEYMFVDNAAMQIIQWPKRFDVMLT 240 Query: 238 ENTFGDILTDEGSVISGSMGLLPSASTGESTPVFEPIHGSWPQAKGLNIANPLAQILSVA 297 EN FGDILTDE SVI+GS+GLLPSAS G T VFEPIHGS+PQA G NIANPLA ILS A Sbjct: 241 ENMFGDILTDEASVITGSLGLLPSASIGVHTSVFEPIHGSYPQAAGKNIANPLATILSAA 300 Query: 298 MLFE-YFDCKAEGALIRKAVDASLDANVRTPEIQVEGGEKFGTKEVGAWIVDYI 350 ++ E F+ K E +IR AV+ASL+ T +I + T EVG WI +YI Sbjct: 301 LMLESAFNLKEEANMIRTAVEASLEQGKVTEDI--DKSNALSTSEVGDWIAEYI 352 Lambda K H 0.319 0.136 0.403 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: 416 Number of extensions: 13 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: 353 Length of database: 355 Length adjustment: 29 Effective length of query: 324 Effective length of database: 326 Effective search space: 105624 Effective search space used: 105624 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_010526307.1 GQW_RS0101545 (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.3087436.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-144 464.8 0.0 9.7e-144 464.6 0.0 1.0 1 NCBI__GCF_000220155.1:WP_010526307.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000220155.1:WP_010526307.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 464.6 0.0 9.7e-144 9.7e-144 1 345 [. 4 344 .. 4 348 .. 0.97 Alignments for each domain: == domain 1 score: 464.6 bits; conditional E-value: 9.7e-144 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGG 73 +iavLpGDgiGpe+v++a k L+av ++++++ ++ ea +G aid+tg+P peet + c +adavL+ga+G NCBI__GCF_000220155.1:WP_010526307.1 4 NIAVLPGDGIGPEIVEQAKKSLDAVLKKKGHEANYTEAPVGAVAIDQTGDPYPEETHQICMNADAVLFGAIGD 76 69*********************************************************************** PP TIGR00169 74 pkWdnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYfGepker 145 pk+dn p+ +vrPe+gLL++rk+l+l+an+rP++ f+sL++ spl++++v+g D+v +reLtgGiYfG+p++r NCBI__GCF_000220155.1:WP_010526307.1 77 PKYDNDPKaKVRPEQGLLAMRKKLGLYANIRPVTTFPSLIHKSPLRSDLVDGADFVAIRELTGGIYFGRPQGR 149 *****986379************************************************************** PP TIGR00169 146 eeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehly 218 +e+ ++a+dt +Yt+eeieri+r+af a+krrkk+t vDkanvL++srlWr+tv++ia ++ +ve+e ++ NCBI__GCF_000220155.1:WP_010526307.1 150 SED--GRTAYDTNVYTVEEIERITRLAFDFAMKRRKKLTVVDKANVLATSRLWRETVQAIAPDFLEVEVEYMF 220 *95..889***************************************************************** PP TIGR00169 219 iDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianp 291 +Dnaamq+++ P+++dv++t+n+fGDil DeasvitGslGlLPsas++ + +fep+hgs p+ agk+ianp NCBI__GCF_000220155.1:WP_010526307.1 221 VDNAAMQIIQWPKRFDVMLTENMFGDILTDEASVITGSLGLLPSASIG-VHTSVFEPIHGSYPQAAGKNIANP 292 ************************************************.8899******************** PP TIGR00169 292 iaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstkev 345 +a+ilsaal+l++++nl+e+a++i +av+ le+gk ted+ +++ a st+ev NCBI__GCF_000220155.1:WP_010526307.1 293 LATILSAALMLESAFNLKEEANMIRTAVEASLEQGKVTEDIDKSN--ALSTSEV 344 *****************************************9887..5555555 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: 19.28 // [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