Align 2-(omega-methylthio)alkylmalate dehydratase (subunit 1/2) (EC 4.2.1.170); 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_012475118.1 CPHAMN1_RS08590 3-isopropylmalate dehydratase small subunit
Query= BRENDA::Q9ZW85 (251 letters) >NCBI__GCF_000020545.1:WP_012475118.1 Length = 187 Score = 152 bits (383), Expect = 6e-42 Identities = 85/183 (46%), Positives = 111/183 (60%), Gaps = 8/183 (4%) Query: 72 GLCYVVGDNIDTDQIIPAEFLTLVPSNPEEYEKLGSYALVGLPASYK------ERFVQPG 125 G YV+G NIDTDQIIPAE L S+PEE + G YAL G+P FV Sbjct: 7 GKAYVLGKNIDTDQIIPAEHLVYSLSDPEEVKLYGRYALSGVPVDEAGLPEGGHPFVAED 66 Query: 126 EMKTKYSIIIGGENFGCGSSREHAPVCLGAAGAKAVVAQSYARIFFRNSVATGEVYPLDS 185 ++ YSIII G NFGCGSSREHAP L AG +A+VA+SYARIF+RN V G V P ++ Sbjct: 67 RFESDYSIIIAGPNFGCGSSREHAPFSLQVAGVRAIVAESYARIFYRNCVDGGFVIPYET 126 Query: 186 EVRVCDECTTGDVATVELREGDSILINHTTGKEYKLKPIGDAGPVIDAGGIFAYARKAGM 245 ++ TGD +++ + + + N T G Y+L P+GD ++ AGGIF YAR+ + Sbjct: 127 AEQLNKTVLTGDDLKIDIEK--NTITNLTQGITYELNPLGDVFNIVMAGGIFEYARQNNI 184 Query: 246 IPS 248 I S Sbjct: 185 INS 187 Lambda K H 0.316 0.132 0.378 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: 151 Number of extensions: 8 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: 251 Length of database: 187 Length adjustment: 22 Effective length of query: 229 Effective length of database: 165 Effective search space: 37785 Effective search space used: 37785 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: 45 (21.9 bits)
Align candidate WP_012475118.1 CPHAMN1_RS08590 (3-isopropylmalate dehydratase small subunit)
to HMM TIGR02087 (3-isopropylmalate dehydratase, small subunit)
# 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/TIGR02087.hmm # target sequence database: /tmp/gapView.17806.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02087 [M=157] Accession: TIGR02087 Description: LEUD_arch: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-37 115.3 0.0 1.4e-36 111.7 0.0 1.9 1 lcl|NCBI__GCF_000020545.1:WP_012475118.1 CPHAMN1_RS08590 3-isopropylmalat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020545.1:WP_012475118.1 CPHAMN1_RS08590 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 111.7 0.0 1.4e-36 1.4e-36 1 156 [. 7 181 .. 7 182 .. 0.80 Alignments for each domain: == domain 1 score: 111.7 bits; conditional E-value: 1.4e-36 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrtt..d...lkelakhamegidpe..........fakkvr...eGdvi 51 G+++ +G ++dtd+iiP++ l + d +k ++++a+ g+ + f + r + +i lcl|NCBI__GCF_000020545.1:WP_012475118.1 7 GKAYVLGKNIDTDQIIPAEHLVYSlsDpeeVKLYGRYALSGVPVDeaglpegghpFVAEDRfesDYSII 75 89****************998653224112556799***9985332222223333444333211456** PP TIGR02087 52 vaGknfGiGssreqaalalkaaGvaaviaesfarifyrnainvG..lplivaedvtelikdGdevevdl 118 +aG nfG+Gssre+a+++l+ aGv+a++aes+arifyrn ++ G +p ae+ +++ Gd +++d+ lcl|NCBI__GCF_000020545.1:WP_012475118.1 76 IAGPNFGCGSSREHAPFSLQVAGVRAIVAESYARIFYRNCVDGGfvIPYETAEQLNKTVLTGDDLKIDI 144 ******************************************9943345566677888889******** PP TIGR02087 119 ekgeirkvakkevlkleeledllleileeGGlleylkk 156 ek+ i ++++ +++l++l d+ +i+ +GG+ ey ++ lcl|NCBI__GCF_000020545.1:WP_012475118.1 145 EKNTITNLTQGITYELNPLGDV-FNIVMAGGIFEYARQ 181 *******************997.6899********987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (187 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 1.18 // [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