Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_086508767.1 BZY95_RS04410 3-isopropylmalate dehydrogenase
Query= SwissProt::Q56268 (358 letters) >NCBI__GCF_002151265.1:WP_086508767.1 Length = 359 Score = 443 bits (1139), Expect = e-129 Identities = 234/354 (66%), Positives = 274/354 (77%), Gaps = 3/354 (0%) Query: 2 KKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQL 61 +KI + GDGIGPEI A A ++L A QA L + +GLVGG+A D +PLPA +L Sbjct: 3 RKILVLPGDGIGPEITAEASRILAAC-QAHGLDIEIEQGLVGGSAYDEHGEPLPAVTLDK 61 Query: 62 AMAADAVILGAVGGPRWDAYPP-AKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLR 120 A AADA++LGAVGGP+WD AKRPE+GLL LRK L L+ANLRPA +PQL AS L+ Sbjct: 62 AKAADAILLGAVGGPKWDKLEDLAKRPEKGLLGLRKNLGLFANLRPAITYPQLASASSLK 121 Query: 121 PELVRDVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRAAQG 180 PELV +DI++VRELTG IYFGQPRG+EV DG+R GFNT +Y E EI RI VAF AQ Sbjct: 122 PELVAGLDIMIVRELTGGIYFGQPRGIEVRDGQRVGFNTYIYSESEIERIGRVAFELAQK 181 Query: 181 RRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLT 240 R K+LCSVDKANVLE T LWREV+ +A +YPDV LSHMYVDNAAMQL+RAP QFDV++T Sbjct: 182 RGKRLCSVDKANVLEVTILWREVMERLAPEYPDVELSHMYVDNAAMQLVRAPKQFDVMVT 241 Query: 241 GNMFGDILSDEASQLTGSIGMLPSASLGE-GRAMYEPIHGSAPDIAGQDKANPLATILSV 299 GNMFGDILSD A+ LTGSIGMLPSASL E G+ MYEP HGSAPDIAG+ ANPLATILSV Sbjct: 242 GNMFGDILSDAAAMLTGSIGMLPSASLNESGQGMYEPCHGSAPDIAGKGIANPLATILSV 301 Query: 300 AMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNA 353 AMMLR+SL +A R+EAAV +VLD GLRTADIA+ GT + T+ MG AV+ A Sbjct: 302 AMMLRYSLGEPEFAGRIEAAVGKVLDDGLRTADIASEGTRTVSTREMGDAVLAA 355 Lambda K H 0.320 0.137 0.396 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: 429 Number of extensions: 17 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: 358 Length of database: 359 Length adjustment: 29 Effective length of query: 329 Effective length of database: 330 Effective search space: 108570 Effective search space used: 108570 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_086508767.1 BZY95_RS04410 (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.15526.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-156 504.1 0.0 1.1e-155 503.9 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508767.1 BZY95_RS04410 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508767.1 BZY95_RS04410 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 503.9 0.0 1.1e-155 1.1e-155 1 348 [. 4 351 .. 4 352 .. 0.98 Alignments for each domain: == domain 1 score: 503.9 bits; conditional E-value: 1.1e-155 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 ki vLpGDgiGpe++aea ++L a + ++l++e e+ l+GG a d++gePlp+ tl+++k+ada+Llg lcl|NCBI__GCF_002151265.1:WP_086508767.1 4 KILVLPGDGIGPEITAEASRILAACQ-AHGLDIEIEQGLVGGSAYDEHGEPLPAVTLDKAKAADAILLG 71 799*******************9987.579*************************************** PP TIGR00169 70 avGGpkWdnlpr.dvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGi 137 avGGpkWd+l +rPekgLL lrk+l+lfanLrPa +++L ++s+lk+e+v g+D+++vreLtgGi lcl|NCBI__GCF_002151265.1:WP_086508767.1 72 AVGGPKWDKLEDlAKRPEKGLLGLRKNLGLFANLRPAITYPQLASASSLKPELVAGLDIMIVRELTGGI 140 *********964378****************************************************** PP TIGR00169 138 YfGepkereeaeeekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206 YfG+p+++e + ++ +++t Y+++eieri rvafela+kr k+++svDkanvLe+++lWr+++e +a lcl|NCBI__GCF_002151265.1:WP_086508767.1 141 YFGQPRGIEVRDGQRVGFNTYIYSESEIERIGRVAFELAQKRGKRLCSVDKANVLEVTILWREVMERLA 209 **********999******************************************************** PP TIGR00169 207 keyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275 eyPdvel+h+y+DnaamqLv++P+q+dv+vt+n+fGDilsD a+++tGs+G+LPsasl+++g++++ep lcl|NCBI__GCF_002151265.1:WP_086508767.1 210 PEYPDVELSHMYVDNAAMQLVRAPKQFDVMVTGNMFGDILSDAAAMLTGSIGMLPSASLNESGQGMYEP 278 ********************************************************************* PP TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344 hgsapdiagkgianp+a+ils+a++lrysl+ +e a +ieaav kvl++g rt+d+ase+t +vst+e lcl|NCBI__GCF_002151265.1:WP_086508767.1 279 CHGSAPDIAGKGIANPLATILSVAMMLRYSLGEPEFAGRIEAAVGKVLDDGLRTADIASEGTRTVSTRE 347 ********************************************************************* PP TIGR00169 345 veee 348 +++ lcl|NCBI__GCF_002151265.1:WP_086508767.1 348 MGDA 351 *986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (359 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: 12.08 // [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