Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate PP_1986 PP_1986 3-isopropylmalate dehydratase small subunit
Query= uniprot:Q845W4 (216 letters) >FitnessBrowser__Putida:PP_1986 Length = 214 Score = 325 bits (832), Expect = 5e-94 Identities = 154/210 (73%), Positives = 176/210 (83%) Query: 1 MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60 M+ FT HTG+VAPLDR NVDTD IIPKQFLKSIKRTGFGPN FDEWRYLD G+P QDNSK Sbjct: 1 MKAFTQHTGIVAPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPYQDNSK 60 Query: 61 RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120 RPLN +FVLN RYQGAS+L+ R+NFGCGSSREHAPWAL +YGFR+IIAPSFADIFFNN Sbjct: 61 RPLNEEFVLNHARYQGASVLLARENFGCGSSREHAPWALDEYGFRSIIAPSFADIFFNNS 120 Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180 FKNGLLPI+L++++VD L + A GYQLTIDL+AQ V PDG+ FEI AFRK+CLL Sbjct: 121 FKNGLLPIILSDEEVDELFKQVEANPGYQLTIDLQAQAVTRPDGKVLHFEIDAFRKHCLL 180 Query: 181 NGFDDIGLTLRHADKIRQFEAERLAKQPWL 210 NG DDIGLTL+ +D I+ FEA+ A QPWL Sbjct: 181 NGLDDIGLTLQDSDAIKAFEAKHRASQPWL 210 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: 233 Number of extensions: 3 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: 216 Length of database: 214 Length adjustment: 22 Effective length of query: 194 Effective length of database: 192 Effective search space: 37248 Effective search space used: 37248 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 PP_1986 PP_1986 (3-isopropylmalate dehydratase small subunit)
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.30434.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-94 299.0 0.0 8.8e-94 298.7 0.0 1.1 1 lcl|FitnessBrowser__Putida:PP_1986 PP_1986 3-isopropylmalate dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1986 PP_1986 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 298.7 0.0 8.8e-94 8.8e-94 1 188 [] 1 196 [. 1 196 [. 0.94 Alignments for each domain: == domain 1 score: 298.7 bits; conditional E-value: 8.8e-94 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryld......ekGkep.npefvlnvpqyq 68 mk f ++tG+v+pld+anvdtd+iipkqflk ikrtGfg +lf ewryld ++ k p n efvln+ +yq lcl|FitnessBrowser__Putida:PP_1986 1 MKAFTQHTGIVAPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDvgqpyqDNSKRPlNEEFVLNHARYQ 75 899*********************************************98333322233333488********** PP TIGR00171 69 gasillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkl 142 gas+llarenfGcGssrehapwal++yGf++iiapsfadif+nnsfkngllpi ls+eev+el+++v+ n+g +l lcl|FitnessBrowser__Putida:PP_1986 76 GASVLLARENFGCGSSREHAPWALDEYGFRSIIAPSFADIFFNNSFKNGLLPIILSDEEVDELFKQVEaNPGYQL 150 *******************************************************************99****** PP TIGR00171 143 tvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188 t+dl+aq v+ +gkv +feid+frkhcllnGld+igltlq d+i lcl|FitnessBrowser__Putida:PP_1986 151 TIDLQAQAVTRPDGKVLHFEIDAFRKHCLLNGLDDIGLTLQDSDAI 196 ******************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (214 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: 6.47 // [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