Align 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (characterized)
to candidate 8501058 DvMF_1794 3-isopropylmalate dehydrogenase (RefSeq)
Query= BRENDA::P93832 (405 letters) >FitnessBrowser__Miya:8501058 Length = 358 Score = 414 bits (1065), Expect = e-120 Identities = 219/354 (61%), Positives = 259/354 (73%), Gaps = 1/354 (0%) Query: 45 ITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETISAAK 104 I L+PGDGIGPE+V A VL + G ++ IGGAA+D G PLP+ET++A K Sbjct: 5 ICLMPGDGIGPEIVEQAVKVLDKVAKKFGHTVSYTNALIGGAAIDATGGPLPDETVAACK 64 Query: 105 ESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLKREV 164 +DAVLLGA+GG KWD +RPEKGLL IR AL +FANLRPAT+LP+L A L+ ++ Sbjct: 65 AADAVLLGAVGGPKWDTLPTAIRPEKGLLGIRKALGLFANLRPATLLPELAGACLLRADI 124 Query: 165 A-EGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETARKR 223 A +G+D+MVVRELTGG+YFGEP + +G +NT +Y E+ RIARVAFE ARKR Sbjct: 125 AAQGLDVMVVRELTGGVYFGEPVCEEELRDGLRTSYNTMIYNEEEVRRIARVAFEAARKR 184 Query: 224 RGKLCSVDKANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTN 283 K+CSVDKANVL S LWR V +A EYPDVEL+HMYVDNAAMQLVR P QFD IVT Sbjct: 185 SRKVCSVDKANVLAVSRLWRAVVIEVAREYPDVELTHMYVDNAAMQLVRWPAQFDVIVTE 244 Query: 284 NIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILSAA 343 N+FGDILSDEA++ITGSIGMLPSASL SGPG+FEPIHGSAPDIAGQ+KANP+ATILS A Sbjct: 245 NLFGDILSDEAAVITGSIGMLPSASLGASGPGIFEPIHGSAPDIAGQNKANPVATILSVA 304 Query: 344 MLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKSV 397 M+L+Y G EK A IE AV L G+RTGDI G LVG MG V + V Sbjct: 305 MMLRYTFGLEKEAVAIEQAVSGVLREGYRTGDIMEEGKTLVGTVSMGNLVTERV 358 Lambda K H 0.316 0.134 0.374 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: 417 Number of extensions: 8 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: 405 Length of database: 358 Length adjustment: 30 Effective length of query: 375 Effective length of database: 328 Effective search space: 123000 Effective search space used: 123000 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate 8501058 DvMF_1794 (3-isopropylmalate dehydrogenase (RefSeq))
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.29902.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-162 526.9 0.0 1.3e-162 526.7 0.0 1.0 1 lcl|FitnessBrowser__Miya:8501058 DvMF_1794 3-isopropylmalate dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501058 DvMF_1794 3-isopropylmalate dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 526.7 0.0 1.3e-162 1.3e-162 1 347 [. 4 352 .. 4 354 .. 0.98 Alignments for each domain: == domain 1 score: 526.7 bits; conditional E-value: 1.3e-162 TIGR00169 1 kiavLpGDgiGpevvaealkvLkaveerfelklefeealiGGaaidatgePlpeetlkackeadavLlgavGGpkWd 77 ki ++pGDgiGpe+v++a+kvL++v+++f++ + + +aliGGaaidatg Plp+et++ack+adavLlgavGGpkWd lcl|FitnessBrowser__Miya:8501058 4 KICLMPGDGIGPEIVEQAVKVLDKVAKKFGHTVSYTNALIGGAAIDATGGPLPDETVAACKAADAVLLGAVGGPKWD 80 799************************************************************************** PP TIGR00169 78 nlprdvrPekgLLklrkeldlfanLrPaklfksLeklsplkeeiv.kgvDlvvvreLtgGiYfGepkereeaee.ek 152 +lp+ +rPekgLL +rk l+lfanLrPa+l ++L ++ l+++i+ +g+D++vvreLtgG+YfGep +ee + + lcl|FitnessBrowser__Miya:8501058 81 TLPTAIRPEKGLLGIRKALGLFANLRPATLLPELAGACLLRADIAaQGLDVMVVRELTGGVYFGEPVCEEELRDgLR 157 ********************************************989*******************99988777799 PP TIGR00169 153 kaldtekYtkeeieriarvafelarkrrkkvtsvDkanvLessrlWrktveeiakeyPdvelehlyiDnaamqLvks 229 ++++t+ Y++ee++riarvafe+arkr +kv+svDkanvL++srlWr +v e+a+eyPdvel h+y+DnaamqLv+ lcl|FitnessBrowser__Miya:8501058 158 TSYNTMIYNEEEVRRIARVAFEAARKRSRKVCSVDKANVLAVSRLWRAVVIEVAREYPDVELTHMYVDNAAMQLVRW 234 9**************************************************************************** PP TIGR00169 230 PeqldvvvtsnlfGDilsDeasvitGslGlLPsaslsskglalfepvhgsapdiagkgianpiaailsaalllrysl 306 P+q+dv+vt+nlfGDilsDea+vitGs+G+LPsasl+ +g ++fep+hgsapdiag++ anp+a+ils+a++lry++ lcl|FitnessBrowser__Miya:8501058 235 PAQFDVIVTENLFGDILSDEAAVITGSIGMLPSASLGASGPGIFEPIHGSAPDIAGQNKANPVATILSVAMMLRYTF 311 ***************************************************************************** PP TIGR00169 307 nleeaaeaieaavkkvleegkrtedlaseattavstkevee 347 +le++a aie+av+ vl+eg+rt d+++e+ t v+t ++++ lcl|FitnessBrowser__Miya:8501058 312 GLEKEAVAIEQAVSGVLREGYRTGDIMEEGKTLVGTVSMGN 352 **********************************9998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (349 nodes) Target sequences: 1 (358 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: 11.23 // [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