Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate WP_012409328.1 NPUN_RS14260 3-isopropylmalate dehydrogenase
Query= BRENDA::Q00412 (355 letters) >NCBI__GCF_000020025.1:WP_012409328.1 Length = 362 Score = 550 bits (1416), Expect = e-161 Identities = 278/352 (78%), Positives = 305/352 (86%) Query: 1 MTQNYRITLLSGDGIGPEIMAVAVDVLKAVGKQLDLNFEFKEALMGGVAIDATGEPLPEE 60 MTQNYRITLL GDGIGPEIMAVAVDVLK VGKQ DL FEF+EAL+GG AIDATGEPLP Sbjct: 1 MTQNYRITLLPGDGIGPEIMAVAVDVLKVVGKQFDLKFEFQEALIGGAAIDATGEPLPSA 60 Query: 61 SLQACRDSDAVLLAAIGGYKWDNLPRPERPETGLLALRAGLGLFANRARLLFCPHVLDAS 120 +L+ CR+SDAVLLAAIGGYKWD+LP RPE GLL LRAGLGLFAN P ++DAS Sbjct: 61 TLETCRNSDAVLLAAIGGYKWDSLPSNLRPEAGLLGLRAGLGLFANLRPAKILPQLIDAS 120 Query: 121 SLKREVVEGVDIMVVRELTGGIYFGQPKGIFETETGKNEGSNTMAYGESEIDRIGRVGFE 180 +LKREVVEGVDIMVVRELTGGIYFG+PKGIF TETG+ G NTM Y ESEI+RIGRV FE Sbjct: 121 TLKREVVEGVDIMVVRELTGGIYFGKPKGIFATETGEKRGVNTMVYTESEIERIGRVAFE 180 Query: 181 TAKKRQGRLCSVDKANVLDVSQLWRDRIMALAADYPEVELSHLYVDNAAMQLVRWPKQFD 240 A+KR G+LCSVDKANVL+VSQLWRDRI L+ +YP++ELSHLYVDNAAMQLVR PKQFD Sbjct: 181 AARKRGGKLCSVDKANVLEVSQLWRDRITQLSQEYPDIELSHLYVDNAAMQLVRAPKQFD 240 Query: 241 TIVTGNLFGDILSDAAAMLTGSIGMLPSASLGASGPGVFEPVHGSAPDIAGQDKANPLAQ 300 TIVTGNLFGDILSDAAAMLTGSIGMLPSASLGASGPGVFEPVHGSAPDIAGQDKANPLAQ Sbjct: 241 TIVTGNLFGDILSDAAAMLTGSIGMLPSASLGASGPGVFEPVHGSAPDIAGQDKANPLAQ 300 Query: 301 VLSAAMMLRYGLDEPAASDPVEKAVLKVLDWGYPTGDIMSEGMKAVGCRKWG 352 VLSAAMMLRY LD+P A+D +E+AV +VL+ G TGDI+S G +GCR G Sbjct: 301 VLSAAMMLRYALDQPKAADRIEQAVFQVLEQGDRTGDIISPGKNLLGCRAMG 352 Lambda K H 0.318 0.137 0.407 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: 511 Number of extensions: 20 Number of successful extensions: 1 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: 355 Length of database: 362 Length adjustment: 29 Effective length of query: 326 Effective length of database: 333 Effective search space: 108558 Effective search space used: 108558 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_012409328.1 NPUN_RS14260 (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.26212.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-166 537.6 0.0 7.2e-166 537.4 0.0 1.0 1 lcl|NCBI__GCF_000020025.1:WP_012409328.1 NPUN_RS14260 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020025.1:WP_012409328.1 NPUN_RS14260 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 537.4 0.0 7.2e-166 7.2e-166 1 348 [. 6 354 .. 6 355 .. 0.99 Alignments for each domain: == domain 1 score: 537.4 bits; conditional E-value: 7.2e-166 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 +i++LpGDgiGpe++a a++vLk+v ++f+lk+ef+ealiGGaaidatgePlp +tl++c+++davLl+ lcl|NCBI__GCF_000020025.1:WP_012409328.1 6 RITLLPGDGIGPEIMAVAVDVLKVVGKQFDLKFEFQEALIGGAAIDATGEPLPSATLETCRNSDAVLLA 74 699****************************************************************** PP TIGR00169 70 avGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138 a+GG+kWd+lp++ rPe gLL lr l+lfanLrPak+ ++L+++s+lk+e+v+gvD++vvreLtgGiY lcl|NCBI__GCF_000020025.1:WP_012409328.1 75 AIGGYKWDSLPSNLRPEAGLLGLRAGLGLFANLRPAKILPQLIDASTLKREVVEGVDIMVVRELTGGIY 143 ********************************************************************* PP TIGR00169 139 fGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206 fG+pk+++ +e+ ek++++t++Yt++eieri rvafe+arkr k++svDkanvLe+s+lWr++++++ lcl|NCBI__GCF_000020025.1:WP_012409328.1 144 FGKPKGIFATETgEKRGVNTMVYTESEIERIGRVAFEAARKRGGKLCSVDKANVLEVSQLWRDRITQLS 212 *********9999******************************************************** PP TIGR00169 207 keyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275 +eyPd+el+hly+DnaamqLv++P+q+d++vt+nlfGDilsD a+++tGs+G+LPsasl+ +g ++fep lcl|NCBI__GCF_000020025.1:WP_012409328.1 213 QEYPDIELSHLYVDNAAMQLVRAPKQFDTIVTGNLFGDILSDAAAMLTGSIGMLPSASLGASGPGVFEP 281 ********************************************************************* PP TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344 vhgsapdiag++ anp+a++lsaa++lry+l++++aa++ie+av +vle+g rt d+ s + + ++++ lcl|NCBI__GCF_000020025.1:WP_012409328.1 282 VHGSAPDIAGQDKANPLAQVLSAAMMLRYALDQPKAADRIEQAVFQVLEQGDRTGDIISPGKNLLGCRA 350 *************************************************************99999999 PP TIGR00169 345 veee 348 ++++ lcl|NCBI__GCF_000020025.1:WP_012409328.1 351 MGDS 354 9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (362 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.49 // [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