Align 3-isopropylmalate dehydratase small subunit; EC 4.2.1.33 (characterized, see rationale)
to candidate WP_057509304.1 ABB28_RS14505 3-isopropylmalate dehydratase small subunit
Query= uniprot:Q845W4 (216 letters) >NCBI__GCF_001431535.1:WP_057509304.1 Length = 192 Score = 171 bits (432), Expect = 1e-47 Identities = 91/202 (45%), Positives = 114/202 (56%), Gaps = 13/202 (6%) Query: 1 MEKFTVHTGVVAPLDRENVDTDAIIPKQFLKSIKRTGFGPNAFDEWRYLDHGEPGQDNSK 60 M F L + N+DTD IIP +FL + +R G G NAF++WR+ G P Sbjct: 1 MSGFRTLASASVVLRQTNIDTDQIIPARFLSTTERAGLGRNAFNDWRWTSDGTP------ 54 Query: 61 RPLNPDFVLNQPRYQGASILVTRKNFGCGSSREHAPWALQQYGFRAIIAPSFADIFFNNC 120 N DF NQP+ G SIL+ +NFGCGSSREHAPWAL G RAI++ ADIF N Sbjct: 55 ---NADFAFNQPQNAGRSILLAGRNFGCGSSREHAPWALTDLGLRAIVSSEIADIFRGNS 111 Query: 121 FKNGLLPIVLTEQQVDHLINETVAFNGYQLTIDLEAQVVRTPDGRDYPFEITAFRKYCLL 180 KNGLLP+VL E V L+ LTID+ A+ +RTPDGR Y F + F + CLL Sbjct: 112 LKNGLLPVVLDEADVQALMQRP----DDVLTIDIAARELRTPDGRVYTFPLDGFSQTCLL 167 Query: 181 NGFDDIGLTLRHADKIRQFEAE 202 G D +G L I ++E E Sbjct: 168 EGVDQLGYLLGRVPDIERYETE 189 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: 149 Number of extensions: 4 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: 216 Length of database: 192 Length adjustment: 21 Effective length of query: 195 Effective length of database: 171 Effective search space: 33345 Effective search space used: 33345 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 WP_057509304.1 ABB28_RS14505 (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.3658.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-60 189.0 0.0 4.4e-60 188.8 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509304.1 ABB28_RS14505 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057509304.1 ABB28_RS14505 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 188.8 0.0 4.4e-60 4.4e-60 1 182 [. 1 177 [. 1 183 [. 0.95 Alignments for each domain: == domain 1 score: 188.8 bits; conditional E-value: 4.4e-60 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqg 69 m +f++l +v+l + n+dtd+iip +fl + +r G+g+++f++wr+ ++G pn++f +n+pq g lcl|NCBI__GCF_001431535.1:WP_057509304.1 1 MSGFRTLASASVVLRQTNIDTDQIIPARFLSTTERAGLGRNAFNDWRW-TSDG-TPNADFAFNQPQNAG 67 78999*******************************************.6677.8************** PP TIGR00171 70 asillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvknk 138 silla+ nfGcGssrehapwal+d G++ i++ adif +ns+kngllp+ l+e++v+ l++ + lcl|NCBI__GCF_001431535.1:WP_057509304.1 68 RSILLAGRNFGCGSSREHAPWALTDLGLRAIVSSEIADIFRGNSLKNGLLPVVLDEADVQALMQ---RP 133 *********************************************************9998876...56 PP TIGR00171 139 glkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltl 182 lt+d+ a+++++ +g+vy+f +d f + cll+G+d++g l lcl|NCBI__GCF_001431535.1:WP_057509304.1 134 DDVLTIDIAARELRTPDGRVYTFPLDGFSQTCLLEGVDQLGYLL 177 778************************************99766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (192 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: 00:00:00.00 # Mc/sec: 6.74 // [ok]
This GapMind analysis is from Apr 10 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