Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate WP_101445098.1 BD749_RS13370 3-isopropylmalate dehydratase small subunit
Query= uniprot:A0A1X9Z766 (195 letters) >NCBI__GCF_002846395.1:WP_101445098.1 Length = 198 Score = 260 bits (665), Expect = 1e-74 Identities = 123/194 (63%), Positives = 153/194 (78%) Query: 1 MKKFTKLTSAVVPLNIENIDTDQIIPARFLKATTREGFGENLFRDWRYENDNQPKADFVM 60 M+KF + + VPL IENIDTDQIIPARFLKAT+REGFGENLFRDWRY + +PK DFV+ Sbjct: 1 MEKFEIIRTGAVPLPIENIDTDQIIPARFLKATSREGFGENLFRDWRYSSSGEPKRDFVL 60 Query: 61 NNPTYSGQVLVAGKNFGCGSSREHAAWAIQDAGFDAVISSFFADIFKGNALNNGLLPIQV 120 NN Y GQVL+AGKNFGCGSSREHAAWAI DAGF VISS+FADIF+GNALNNGLLP+QV Sbjct: 61 NNSRYKGQVLLAGKNFGCGSSREHAAWAIYDAGFRVVISSYFADIFRGNALNNGLLPLQV 120 Query: 121 SDEFLAQIFKAVDNNPKSALEVDLENQTVTIVETGAQESFEINPYKKSCLINGYDDIDFI 180 +DE L ++F V+ +P++ ++L Q + + +G + F I+PYKK CLI GYDDIDF+ Sbjct: 121 TDEVLQRLFALVEADPQTEFVINLPEQELYLPASGERIPFAIDPYKKECLIKGYDDIDFL 180 Query: 181 LNQKQLIEEFEEGR 194 ++QK+ I +E R Sbjct: 181 VSQKEAITAYESTR 194 Lambda K H 0.318 0.135 0.393 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: 199 Number of extensions: 4 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: 195 Length of database: 198 Length adjustment: 20 Effective length of query: 175 Effective length of database: 178 Effective search space: 31150 Effective search space used: 31150 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 (21.7 bits) S2: 45 (21.9 bits)
Align candidate WP_101445098.1 BD749_RS13370 (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.3029474.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-60 188.0 0.0 8.4e-60 187.9 0.0 1.0 1 NCBI__GCF_002846395.1:WP_101445098.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101445098.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 187.9 0.0 8.4e-60 8.4e-60 1 188 [] 1 187 [. 1 187 [. 0.94 Alignments for each domain: == domain 1 score: 187.9 bits; conditional E-value: 8.4e-60 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqgasil 73 m++f +vpl n+dtd+iip +flk+ r Gfg++lf +wry + G ep+ +fvln +y+g ++l NCBI__GCF_002846395.1:WP_101445098.1 1 MEKFEIIRTGAVPLPIENIDTDQIIPARFLKATSREGFGENLFRDWRY-SSSG-EPKRDFVLNNSRYKG-QVL 70 677777777899************************************.6778.9************98.799 PP TIGR00171 74 larenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.nkglkltvd 145 la++nfGcGssreha wa+ d Gf+v+i+ fadif +n+++ngllp+++++e ++ l+alv+ ++ +++ ++ NCBI__GCF_002846395.1:WP_101445098.1 71 LAGKNFGCGSSREHAAWAIYDAGFRVVISSYFADIFRGNALNNGLLPLQVTDEVLQRLFALVEaDPQTEFVIN 143 **************************************************************989999***** PP TIGR00171 146 leaqkvk.dsegkvysfeidefrkhcllnGldeigltlqkedei 188 l++q++ + g+ + f id+++k+cl+ G+d+i + + ++++i NCBI__GCF_002846395.1:WP_101445098.1 144 LPEQELYlPASGERIPFAIDPYKKECLIKGYDDIDFLVSQKEAI 187 ****98625778**********************9988777765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (198 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: 10.33 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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