Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate RR42_RS24180 RR42_RS24180 3-isopropylmalate dehydratase
Query= uniprot:Q845W4 (216 letters) >FitnessBrowser__Cup4G11:RR42_RS24180 Length = 216 Score = 372 bits (954), Expect = e-108 Identities = 175/216 (81%), Positives = 189/216 (87%) Query: 1 MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60 MEKFT+H G+VAPLDR NVDTDAIIPKQFLKSIKRTGFGPN FDEWRY D GEPG DNSK Sbjct: 1 MEKFTIHRGLVAPLDRGNVDTDAIIPKQFLKSIKRTGFGPNLFDEWRYKDVGEPGMDNSK 60 Query: 61 RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120 RPLNPDFVLNQPRYQGASIL+ R+NFGCGSSREHAPWAL QYGF A+IAPSFADIFFNNC Sbjct: 61 RPLNPDFVLNQPRYQGASILLARRNFGCGSSREHAPWALTQYGFHAVIAPSFADIFFNNC 120 Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180 +KNGLLP+VLTEQQVDHL NET AF GYQLTIDL+ Q V T G+ Y F+I FRKYC+L Sbjct: 121 YKNGLLPVVLTEQQVDHLFNETNAFKGYQLTIDLDKQAVITASGQGYEFDIAPFRKYCML 180 Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWLNNKLVG 216 NGFDDI LTLRHADKI+ FEAER+AK PWL +L G Sbjct: 181 NGFDDIRLTLRHADKIKVFEAERVAKMPWLKPRLAG 216 Lambda K H 0.322 0.141 0.437 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: 258 Number of extensions: 6 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: 216 Length of database: 216 Length adjustment: 22 Effective length of query: 194 Effective length of database: 194 Effective search space: 37636 Effective search space used: 37636 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 (21.9 bits) S2: 45 (21.9 bits)
Align candidate RR42_RS24180 RR42_RS24180 (3-isopropylmalate dehydratase)
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))
# 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/TIGR00171.hmm # target sequence database: /tmp/gapView.4581.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00171 [M=188] Accession: TIGR00171 Description: leuD: 3-isopropylmalate dehydratase, small subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-85 270.8 0.0 3.6e-85 270.6 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS24180 RR42_RS24180 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS24180 RR42_RS24180 3-isopropylmalate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 270.6 0.0 3.6e-85 3.6e-85 1 188 [] 1 196 [. 1 196 [. 0.94 Alignments for each domain: == domain 1 score: 270.6 bits; conditional E-value: 3.6e-85 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryld..ekGkep.....npefvl 62 m++f + Glv+pld+ nvdtdaiipkqflk ikrtGfg +lf ewry+d e G ++ np+fvl lcl|FitnessBrowser__Cup4G11:RR42_RS24180 1 MEKFTIHRGLVAPLDRGNVDTDAIIPKQFLKSIKRTGFGPNLFDEWRYKDvgEPGMDNskrplNPDFVL 69 899*********************************************9843234332222359***** PP TIGR00171 63 nvpqyqgasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveel 131 n+p+yqgasillar nfGcGssrehapwal++yGf +iapsfadif+nn++kngllp+ l+e++v++l lcl|FitnessBrowser__Cup4G11:RR42_RS24180 70 NQPRYQGASILLARRNFGCGSSREHAPWALTQYGFHAVIAPSFADIFFNNCYKNGLLPVVLTEQQVDHL 138 ********************************************************************* PP TIGR00171 132 lalvk.nkglkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188 ++ + kg +lt+dl++q v ++ g+ y+f+i +frk c+lnG+d+i ltl++ d+i lcl|FitnessBrowser__Cup4G11:RR42_RS24180 139 FNETNaFKGYQLTIDLDKQAVITASGQGYEFDIAPFRKYCMLNGFDDIRLTLRHADKI 196 **99889*************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (216 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: 00:00:00.00 # Mc/sec: 6.02 // [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