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 NP_661513.1 CT0613 3-isopropylmalate dehydratase small subunit
Query= BRENDA::Q9ZW85 (251 letters) >NCBI__GCF_000006985.1:NP_661513.1 Length = 190 Score = 162 bits (410), Expect = 5e-45 Identities = 91/186 (48%), Positives = 117/186 (62%), Gaps = 8/186 (4%) Query: 72 GLCYVVGDNIDTDQIIPAEFLTLVPSNPEEYEKLGSYALVGLP---ASYKER---FVQPG 125 G YV+G NIDTDQIIPAE L S+PEE + G YAL G+P A E FV+ G Sbjct: 7 GKAYVLGKNIDTDQIIPAEHLVYSLSDPEEVKMYGKYALSGVPIDQAGLPEGNIPFVEEG 66 Query: 126 EMKTKYSIIIGGENFGCGSSREHAPVCLGAAGAKAVVAQSYARIFFRNSVATGEVYPLDS 185 E + YSIII G NFGCGSSREHAP L AGAKA++A+SYARIF+RN V G V P ++ Sbjct: 67 EFTSPYSIIIAGPNFGCGSSREHAPFALKVAGAKAIIAESYARIFYRNCVDGGFVIPFET 126 Query: 186 EVRVCDECTTGDVATVELREGDSILINHTTGKEYKLKPIGDAGPVIDAGGIFAYARKAGM 245 + TGD ++++ ++ L N T Y+L+P+GD ++ AGGIF YARK + Sbjct: 127 AQPLNKSIMTGDELSLDME--NNTLTNLTQNITYELRPLGDVINIVQAGGIFEYARKNNL 184 Query: 246 IPSAAA 251 + S A Sbjct: 185 MASTEA 190 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: 160 Number of extensions: 9 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: 190 Length adjustment: 22 Effective length of query: 229 Effective length of database: 168 Effective search space: 38472 Effective search space used: 38472 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 NP_661513.1 CT0613 (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.16412.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-38 118.0 0.0 9.8e-38 115.5 0.0 1.8 1 lcl|NCBI__GCF_000006985.1:NP_661513.1 CT0613 3-isopropylmalate dehydra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000006985.1:NP_661513.1 CT0613 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 115.5 0.0 9.8e-38 9.8e-38 1 157 [] 7 182 .. 7 182 .. 0.79 Alignments for each domain: == domain 1 score: 115.5 bits; conditional E-value: 9.8e-38 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrtt..d...lkelakhamegidpe..........fakkvreGd......vi 51 G+++ +G ++dtd+iiP++ l + d +k+++k+a+ g+ + f v+eG+ +i lcl|NCBI__GCF_000006985.1:NP_661513.1 7 GKAYVLGKNIDTDQIIPAEHLVYSlsDpeeVKMYGKYALSGVPIDqaglpegnipF---VEEGEftspysII 75 89****************998653224222667899***99854411211122223...555533333339* PP TIGR02087 52 vaGknfGiGssreqaalalkaaGvaaviaesfarifyrnainvGlpl.ivae.dvtelikdGdevevdlekg 121 +aG nfG+Gssre+a++alk aG +a+iaes+arifyrn ++ G+++ +++ + i Gde+++d+e++ lcl|NCBI__GCF_000006985.1:NP_661513.1 76 IAGPNFGCGSSREHAPFALKVAGAKAIIAESYARIFYRNCVDGGFVIpFETAqPLNKSIMTGDELSLDMENN 147 *******************************************964314444145677899*********** PP TIGR02087 122 eirkvakkevlkleeledllleileeGGlleylkkr 157 + +++++ +++l++l d+ ++i+++GG+ ey +k+ lcl|NCBI__GCF_000006985.1:NP_661513.1 148 TLTNLTQNITYELRPLGDV-INIVQAGGIFEYARKN 182 ****************997.69***********995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (190 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: 1.14 // [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