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_011610799.1 TERY_RS04845 3-isopropylmalate dehydratase small subunit
Query= BRENDA::Q9ZW85 (251 letters) >NCBI__GCF_000014265.1:WP_011610799.1 Length = 183 Score = 225 bits (574), Expect = 4e-64 Identities = 110/179 (61%), Positives = 138/179 (77%), Gaps = 3/179 (1%) Query: 68 KTFHGLCYVVGDNIDTDQIIPAEFLTLVPSNPEEYEKLGSYALVGLPASYKERFVQPGEM 127 K+ G +V+ DNIDTDQIIPAE+LTLVPS P+EY+KLG+YAL GLP Y RF++P M Sbjct: 3 KSLTGKIFVLDDNIDTDQIIPAEYLTLVPSKPDEYDKLGTYALCGLPDRYG-RFMEPEAM 61 Query: 128 KTKYSIIIGGENFGCGSSREHAPVCLGAAGAKAVVAQSYARIFFRNSVATGEVYPLDSEV 187 KTKY II+ GENFGCGSSREHAP+ LGA+G +AVVAQSYARIFFRN ATGE+YP +S Sbjct: 62 KTKYPIIVAGENFGCGSSREHAPIALGASGVQAVVAQSYARIFFRNCSATGELYPWESSD 121 Query: 188 RVCDECTTGDVATVELREGDSILINHTTGKEYKLKPIGDAGPVIDAGGIFAYARKAGMI 246 R+C+ TG T++ + ++NHT + Y+LK +G+ PVIDAGG+FAYAR+ GMI Sbjct: 122 RLCELFKTGQKVTIDFEKNQ--IVNHTLDQTYQLKSLGEVRPVIDAGGLFAYARQTGMI 178 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: 183 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: 183 Length adjustment: 22 Effective length of query: 229 Effective length of database: 161 Effective search space: 36869 Effective search space used: 36869 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_011610799.1 TERY_RS04845 (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.23542.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-39 121.0 0.0 2.3e-39 120.7 0.0 1.1 1 lcl|NCBI__GCF_000014265.1:WP_011610799.1 TERY_RS04845 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011610799.1 TERY_RS04845 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 120.7 0.0 2.3e-39 2.3e-39 1 156 [. 7 174 .. 7 175 .. 0.84 Alignments for each domain: == domain 1 score: 120.7 bits; conditional E-value: 2.3e-39 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrtt.....dlkelakhamegidpefakkvr......eGdvivaGknfG 58 G+++ + d++dtd+iiP++yl ++ ++++l+++a+ g+ + + + ++ + +ivaG+nfG lcl|NCBI__GCF_000014265.1:WP_011610799.1 7 GKIFVLDDNIDTDQIIPAEYLTLVpskpdEYDKLGTYALCGLPDRYGRFMEpeamktKYPIIVAGENFG 75 899*****************9765333325899********98877554331111114569******** PP TIGR02087 59 iGssreqaalalkaaGvaaviaesfarifyrnainvG.lplivae.dvtelikdGdevevdlekgeirk 125 +Gssre+a++al a Gv+av+a+s+arif+rn +G l + + el k G++v++d+ek++i++ lcl|NCBI__GCF_000014265.1:WP_011610799.1 76 CGSSREHAPIALGASGVQAVVAQSYARIFFRNCSATGeLYPWESSdRLCELFKTGQKVTIDFEKNQIVN 144 ********************************99999655555442789******************** PP TIGR02087 126 vakkevlkleeledllleileeGGlleylkk 156 + +++++l++l ++ + ++++GGl y ++ lcl|NCBI__GCF_000014265.1:WP_011610799.1 145 HTLDQTYQLKSLGEV-RPVIDAGGLFAYARQ 174 ***********9886.6899*******9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (183 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: 5.05 // [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