Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate WP_029132623.1 A3GO_RS0105910 3-isopropylmalate dehydrogenase
Query= SwissProt::Q56268 (358 letters) >NCBI__GCF_000428045.1:WP_029132623.1 Length = 360 Score = 429 bits (1104), Expect = e-125 Identities = 225/355 (63%), Positives = 269/355 (75%), Gaps = 2/355 (0%) Query: 2 KKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQL 61 K I + GDGIG EIV A +VL + L + E L+GG A DA+ PLP A+L L Sbjct: 3 KNILVLPGDGIGQEIVTEAVKVLACLRDDYGLDIEMDEALIGGTAYDAAGHPLPEATLNL 62 Query: 62 AMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRP 121 A ADAV+LGAVGGP+W+ + RPE+GLL +RK L L+ANLRPA ++PQL DAS LRP Sbjct: 63 AREADAVLLGAVGGPKWEPLDISVRPEKGLLGIRKELGLFANLRPAILYPQLADASTLRP 122 Query: 122 ELVRDVDILVVRELTGDIYFGQPRGLEVID-GKRRGFNTMVYDEDEIRRIAHVAFRAAQG 180 E+V +DI++VRELTG IYFGQPRG+ V++ G++ GFNT++Y E E+ RI VA A Sbjct: 123 EVVSGLDIMIVRELTGGIYFGQPRGVRVLENGEKEGFNTLIYKESEVDRIVRVAMDIAMK 182 Query: 181 RRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLT 240 R K++CSVDKANVLE T +WREV +V DYP+V LSHMYVDNAAMQL+RAP QFDV++T Sbjct: 183 RNKRVCSVDKANVLECTEMWREVAVKVGADYPEVELSHMYVDNAAMQLVRAPKQFDVMVT 242 Query: 241 GNMFGDILSDEASQLTGSIGMLPSASLGE-GRAMYEPIHGSAPDIAGQDKANPLATILSV 299 NMFGDILSD AS LTGSIGMLPSASL E G+ MYEPIHGSAPDIAGQ ANPLATILSV Sbjct: 243 TNMFGDILSDCASMLTGSIGMLPSASLDENGKGMYEPIHGSAPDIAGQGVANPLATILSV 302 Query: 300 AMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354 AMMLR+SL+ + A RVE AV + LDQGLRT DI + GT +GT+AMG AVV AL Sbjct: 303 AMMLRYSLDEDAMADRVEQAVNKTLDQGLRTPDIYSEGTRKVGTEAMGDAVVAAL 357 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: 422 Number of extensions: 15 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: 358 Length of database: 360 Length adjustment: 29 Effective length of query: 329 Effective length of database: 331 Effective search space: 108899 Effective search space used: 108899 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_029132623.1 A3GO_RS0105910 (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.22896.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-159 516.1 0.1 2.4e-159 515.9 0.1 1.0 1 lcl|NCBI__GCF_000428045.1:WP_029132623.1 A3GO_RS0105910 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029132623.1 A3GO_RS0105910 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 515.9 0.1 2.4e-159 2.4e-159 1 348 [. 4 352 .. 4 353 .. 0.99 Alignments for each domain: == domain 1 score: 515.9 bits; conditional E-value: 2.4e-159 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlg 69 +i vLpGDgiG+e+v+ea+kvL +++ ++l++e++ealiGG a da g+Plpe+tl+ ++eadavLlg lcl|NCBI__GCF_000428045.1:WP_029132623.1 4 NILVLPGDGIGQEIVTEAVKVLACLRDDYGLDIEMDEALIGGTAYDAAGHPLPEATLNLAREADAVLLG 72 699****************************************************************** PP TIGR00169 70 avGGpkWdnlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeivkgvDlvvvreLtgGiY 138 avGGpkW+ l +vrPekgLL +rkel+lfanLrPa l+++L ++s+l++e+v+g+D+++vreLtgGiY lcl|NCBI__GCF_000428045.1:WP_029132623.1 73 AVGGPKWEPLDISVRPEKGLLGIRKELGLFANLRPAILYPQLADASTLRPEVVSGLDIMIVRELTGGIY 141 ********************************************************************* PP TIGR00169 139 fGepkereeaee.ekkaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeia 206 fG+p++ + e+ ek++++t Y+++e++ri+rva+ +a+kr+k+v+svDkanvLe +++Wr+++ ++ lcl|NCBI__GCF_000428045.1:WP_029132623.1 142 FGQPRGVRVLENgEKEGFNTLIYKESEVDRIVRVAMDIAMKRNKRVCSVDKANVLECTEMWREVAVKVG 210 ********99999******************************************************** PP TIGR00169 207 keyPdvelehlyiDnaamqLvksPeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfep 275 +yP+vel+h+y+DnaamqLv++P+q+dv+vt n+fGDilsD as++tGs+G+LPsasl ++g++++ep lcl|NCBI__GCF_000428045.1:WP_029132623.1 211 ADYPEVELSHMYVDNAAMQLVRAPKQFDVMVTTNMFGDILSDCASMLTGSIGMLPSASLDENGKGMYEP 279 ********************************************************************* PP TIGR00169 276 vhgsapdiagkgianpiaailsaalllryslnleeaaeaieaavkkvleegkrtedlaseattavstke 344 +hgsapdiag+g+anp+a+ils+a++lrysl+ + a+++e+av+k+l++g rt+d++se+t +v+t++ lcl|NCBI__GCF_000428045.1:WP_029132623.1 280 IHGSAPDIAGQGVANPLATILSVAMMLRYSLDEDAMADRVEQAVNKTLDQGLRTPDIYSEGTRKVGTEA 348 ********************************************************************* PP TIGR00169 345 veee 348 +++ lcl|NCBI__GCF_000428045.1:WP_029132623.1 349 MGDA 352 9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (360 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: 7.82 // [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