Align 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 (characterized)
to candidate 208498 DVU2985 3-isopropylmalate dehydrogenase
Query= SwissProt::Q56268 (358 letters) >MicrobesOnline__882:208498 Length = 357 Score = 432 bits (1110), Expect = e-126 Identities = 218/353 (61%), Positives = 271/353 (76%), Gaps = 2/353 (0%) Query: 4 IAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLAM 63 I + GDGIGPEIVA +VLDAV + + + L+GGAA+DA+ PLP A+++ Sbjct: 5 ICLLPGDGIGPEIVAQGTKVLDAVARRFGHTVSTSSALIGGAAIDATGSPLPDATVEACR 64 Query: 64 AADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPEL 123 +DAV+LGAVGGP+WD P KRPE+GLL +RK L L+ANLRPA +FP+L A LR ++ Sbjct: 65 TSDAVLLGAVGGPKWDDLPSEKRPEKGLLGIRKALGLFANLRPAALFPELAGACLLRADI 124 Query: 124 VR-DVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRAAQGRR 182 +D++VVRELTGD+YFGQP G+E DG R GFNTM+YDEDE+RRIA VAF A+ R+ Sbjct: 125 AAAGLDLVVVRELTGDVYFGQPAGIETRDGLRTGFNTMIYDEDEVRRIARVAFDTARARK 184 Query: 183 KQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLTGN 242 +++CSVDKANVL T+RLWREVV EVARDYPDV LSHMYVDNAAMQL+R PAQFDV++TGN Sbjct: 185 RRVCSVDKANVLATSRLWREVVEEVARDYPDVELSHMYVDNAAMQLVRWPAQFDVIVTGN 244 Query: 243 MFGDILSDEASQLTGSIGMLPSASLGE-GRAMYEPIHGSAPDIAGQDKANPLATILSVAM 301 +FGDILSDEA+ +TGSIGMLPSAS+G G A++EPIHGSAPDIAGQDKANP+ATILSV M Sbjct: 245 LFGDILSDEAAVITGSIGMLPSASMGSGGPALFEPIHGSAPDIAGQDKANPIATILSVGM 304 Query: 302 MLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNAL 354 MLR A ++AAV+RVL +G RT DI G ++GT +MG + + Sbjct: 305 MLRLGFGLAAEADAIDAAVRRVLAEGYRTGDIMENGRTLVGTVSMGNLIAERI 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: 449 Number of extensions: 10 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: 357 Length adjustment: 29 Effective length of query: 329 Effective length of database: 328 Effective search space: 107912 Effective search space used: 107912 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 208498 DVU2985 (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.10003.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-160 517.8 0.0 7.4e-160 517.6 0.0 1.0 1 lcl|MicrobesOnline__882:208498 DVU2985 3-isopropylmalate dehydr Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:208498 DVU2985 3-isopropylmalate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 517.6 0.0 7.4e-160 7.4e-160 1 347 [. 4 351 .. 4 353 .. 0.99 Alignments for each domain: == domain 1 score: 517.6 bits; conditional E-value: 7.4e-160 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWdnl 79 +i +LpGDgiGpe+va+ +kvL+av+ rf++ + +++aliGGaaidatg+Plp++t++ac+ +davLlgavGGpkWd+l lcl|MicrobesOnline__882:208498 4 NICLLPGDGIGPEIVAQGTKVLDAVARRFGHTVSTSSALIGGAAIDATGSPLPDATVEACRTSDAVLLGAVGGPKWDDL 82 699**************************************************************************** PP TIGR00169 80 prdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepkereeaeeekkaldt 157 p+++rPekgLL +rk l+lfanLrPa lf++L ++ l+++i+ g+DlvvvreLtg +YfG+p ++e + +++++t lcl|MicrobesOnline__882:208498 83 PSEKRPEKGLLGIRKALGLFANLRPAALFPELAGACLLRADIAaAGLDLVVVRELTGDVYFGQPAGIETRDGLRTGFNT 161 ******************************************989************************999******* PP TIGR00169 158 ekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvksPeqldvv 236 + Y ++e++riarvaf +ar+r+++v+svDkanvL++srlWr++vee+a++yPdvel+h+y+DnaamqLv+ P+q+dv+ lcl|MicrobesOnline__882:208498 162 MIYDEDEVRRIARVAFDTARARKRRVCSVDKANVLATSRLWREVVEEVARDYPDVELSHMYVDNAAMQLVRWPAQFDVI 240 ******************************************************************************* PP TIGR00169 237 vtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllryslnleeaaeai 315 vt+nlfGDilsDea+vitGs+G+LPsas++s g alfep+hgsapdiag++ anpia+ils+ ++lr +++l +a+ai lcl|MicrobesOnline__882:208498 241 VTGNLFGDILSDEAAVITGSIGMLPSASMGSGGPALFEPIHGSAPDIAGQDKANPIATILSVGMMLRLGFGLAAEADAI 319 ******************************************************************************* PP TIGR00169 316 eaavkkvleegkrtedlaseattavstkevee 347 +aav++vl+eg+rt d+++++ t v+t ++++ lcl|MicrobesOnline__882:208498 320 DAAVRRVLAEGYRTGDIMENGRTLVGTVSMGN 351 *************************9999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (357 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 11.01 // [ok]
This GapMind analysis is from Apr 09 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