Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_012384181.1 BIND_RS06000 3-isopropylmalate dehydrogenase
Query= BRENDA::P24404 (370 letters) >NCBI__GCF_000019845.1:WP_012384181.1 Length = 369 Score = 515 bits (1327), Expect = e-151 Identities = 260/362 (71%), Positives = 298/362 (82%), Gaps = 1/362 (0%) Query: 6 LFLLPGDGIGPEAMTEVRKLIEYMNSAHNAGFTVSEGLVGGSAYDAHGVAISDADMEKAL 65 LF+LPGDGIGPE M EV K+ + +A F + +GLVGGSAYDAHGVAISDADM +A Sbjct: 5 LFVLPGDGIGPEVMAEVEKIASFFTQEGSAAFEIEKGLVGGSAYDAHGVAISDADMARAD 64 Query: 66 AADAILFGAVGGPKWDGVPYEHRPEAGLLRLRKDLELFANLRPAICYPALAAASSLKPEL 125 AADA+L AVGGPKWD VPYE RPEAGLLRLRKDL+LFANLRPA+CYPALA ASSLK EL Sbjct: 65 AADAVLLAAVGGPKWDAVPYEVRPEAGLLRLRKDLKLFANLRPAVCYPALADASSLKREL 124 Query: 126 VEGLDILIVRELTGGVYFGEPKQIIDLGNGQKRGIDTQIYDTFEIERIASVAFELARSRD 185 V+GLD++IVRELTGGVYFGEPKQIIDLGNGQ+R IDTQ+Y+T+EIERI +AFELAR R Sbjct: 125 VDGLDLMIVRELTGGVYFGEPKQIIDLGNGQQRAIDTQVYETYEIERIGRIAFELARKRR 184 Query: 186 NRVCSMEKRNVMKSGVLWNQVVTETHAAKYKDVQLEHMLADAGGMQLVRKPKQFDVIVTD 245 +V S EKRNVM++GVLW+Q++ H ++ DV LEH LADA GMQLVR PKQFDVIVTD Sbjct: 185 KKVTSSEKRNVMRTGVLWHQIINRLHDQEFPDVTLEHQLADALGMQLVRAPKQFDVIVTD 244 Query: 246 NLFGDMLSDVAAMLTGSLGMLPSASLGAPDAKTGKRKAMYEPVHGSAPDIAGKSIANPIA 305 NLFGDMLSDVAAMLTGSLGMLPSASLG D++TGKRKA+YEPVHGSAPDIAGK IANPIA Sbjct: 245 NLFGDMLSDVAAMLTGSLGMLPSASLGEVDSQTGKRKALYEPVHGSAPDIAGKGIANPIA 304 Query: 306 MIASFAMCLRYSFNMVDEATKLEAAIANVLDKGIRTADIMADGCR-QVGTSDMGDAVLAE 364 MIASF M LRYSF++ A +++ AIA L KG+RTADI V T+ MGDA+L E Sbjct: 305 MIASFGMALRYSFDLGALADRIDNAIAATLAKGLRTADIKGSSTEPTVSTTQMGDAILKE 364 Query: 365 FK 366 + Sbjct: 365 LQ 366 Lambda K H 0.319 0.135 0.387 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: 514 Number of extensions: 20 Number of successful extensions: 2 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: 370 Length of database: 369 Length adjustment: 30 Effective length of query: 340 Effective length of database: 339 Effective search space: 115260 Effective search space used: 115260 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_012384181.1 BIND_RS06000 (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.3726.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-138 445.6 0.0 6.6e-138 445.4 0.0 1.0 1 lcl|NCBI__GCF_000019845.1:WP_012384181.1 BIND_RS06000 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019845.1:WP_012384181.1 BIND_RS06000 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.4 0.0 6.6e-138 6.6e-138 2 348 .. 5 360 .. 4 361 .. 0.98 Alignments for each domain: == domain 1 score: 445.4 bits; conditional E-value: 6.6e-138 TIGR00169 2 iavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlga 70 + vLpGDgiGpev+ae k+ +++ ++e e+ l+GG a da+g ++++ ++ +++adavLl+a lcl|NCBI__GCF_000019845.1:WP_012384181.1 5 LFVLPGDGIGPEVMAEVEKIASFFTQEGSAAFEIEKGLVGGSAYDAHGVAISDADMARADAADAVLLAA 73 679****************************************************************** PP TIGR00169 71 vGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiYf 139 vGGpkWd+ p +vrPe gLL+lrk+l+lfanLrPa +++L ++s+lk+e+v+g+Dl++vreLtgG+Yf lcl|NCBI__GCF_000019845.1:WP_012384181.1 74 VGGPKWDAVPYEVRPEAGLLRLRKDLKLFANLRPAVCYPALADASSLKRELVDGLDLMIVRELTGGVYF 142 ********************************************************************* PP TIGR00169 140 Gepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiak 207 Gepk++ + ++ +++a+dt++Y+++eieri r+afelarkrrkkvts +k nv+ ++ lW ++++ ++ lcl|NCBI__GCF_000019845.1:WP_012384181.1 143 GEPKQIIDLGNgQQRAIDTQVYETYEIERIGRIAFELARKRRKKVTSSEKRNVMRTGVLWHQIINRLHD 211 ******999999*******************************************************98 PP TIGR00169 208 .eyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslss......kg 269 e+Pdv+leh++ D+ mqLv++P+q+dv+vt+nlfGD+lsD a+++tGslG+LPsasl++ k+ lcl|NCBI__GCF_000019845.1:WP_012384181.1 212 qEFPDVTLEHQLADALGMQLVRAPKQFDVIVTDNLFGDMLSDVAAMLTGSLGMLPSASLGEvdsqtgKR 280 8***************************************************************99999 PP TIGR00169 270 lalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseatt 338 +al+epvhgsapdiagkgianpia+i s + lrys++l a++i++a++ +l++g rt+d+++++t+ lcl|NCBI__GCF_000019845.1:WP_012384181.1 281 KALYEPVHGSAPDIAGKGIANPIAMIASFGMALRYSFDLGALADRIDNAIAATLAKGLRTADIKGSSTE 349 ****************************************************************99987 PP TIGR00169 339 .avstkeveee 348 +vst+++++ lcl|NCBI__GCF_000019845.1:WP_012384181.1 350 pTVSTTQMGDA 360 35788888775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (369 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: 00:00:00.01 # Mc/sec: 7.48 // [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