Align 3-isopropylmalate dehydratase (EC 4.2.1.33) (characterized)
to candidate WP_015411247.1 MM_RS03370 hypothetical protein
Query= BRENDA::Q58673 (168 letters) >NCBI__GCF_000007065.1:WP_015411247.1 Length = 168 Score = 182 bits (462), Expect = 2e-51 Identities = 91/162 (56%), Positives = 117/162 (72%), Gaps = 4/162 (2%) Query: 1 MRSIIKGRVWKFGNNVDTDAILPARYLVYTKPEELAQFVMTGADPDFPKKVKPGDIIVGG 60 M + IKGRVWKFGN++DTD I+P +YL + A M G DP F KK KPGDIIV G Sbjct: 1 MENPIKGRVWKFGNDIDTDVIIPGKYLRTKDMQVFAAHAMEGIDPGFSKKAKPGDIIVAG 60 Query: 61 KNFGCGSSREHAPLGLKGAGISCVIAESFARIFYRNAINVGLPLIECKGISEKVNEGDEL 120 NFGCGSSRE APL LK AGI+C++A+SFARIF+RNAIN+GLPL+E + EGD++ Sbjct: 61 DNFGCGSSREQAPLALKHAGIACIVAKSFARIFFRNAINIGLPLMEA---DIECEEGDQI 117 Query: 121 EVNLETGEIKNLTTGEVLKGQKLPEFMMEILEAGGLMPYLKK 162 EV+L GE+K G V +G KLP+F++++L GGL+ + KK Sbjct: 118 EVDLLKGEVKVSGKG-VFRGNKLPDFLLDMLTDGGLVAHRKK 158 Lambda K H 0.317 0.139 0.405 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: 128 Number of extensions: 7 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: 168 Length of database: 168 Length adjustment: 18 Effective length of query: 150 Effective length of database: 150 Effective search space: 22500 Effective search space used: 22500 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: 43 (21.2 bits)
Align candidate WP_015411247.1 MM_RS03370 (hypothetical protein)
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.16318.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-76 240.2 0.1 4.6e-76 240.0 0.1 1.0 1 lcl|NCBI__GCF_000007065.1:WP_015411247.1 MM_RS03370 hypothetical protein Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007065.1:WP_015411247.1 MM_RS03370 hypothetical protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 240.0 0.1 4.6e-76 4.6e-76 1 156 [. 7 158 .. 7 159 .. 0.98 Alignments for each domain: == domain 1 score: 240.0 bits; conditional E-value: 4.6e-76 TIGR02087 1 GrvwkfGddvdtdaiiPgrylrttdlkelakhamegidpefakkvreGdvivaGknfGiGssreqaala 69 GrvwkfG+d+dtd+iiPg+ylrt+d++ +a+hamegidp f+kk+++Gd+ivaG nfG+Gssreqa+la lcl|NCBI__GCF_000007065.1:WP_015411247.1 7 GRVWKFGNDIDTDVIIPGKYLRTKDMQVFAAHAMEGIDPGFSKKAKPGDIIVAGDNFGCGSSREQAPLA 75 9******************************************************************** PP TIGR02087 70 lkaaGvaaviaesfarifyrnainvGlplivaedvtelikdGdevevdlekgeirkvakkevlkleele 138 lk+aG+a+++a+sfarif+rnain+Glpl++a+ +e+ +Gd++evdl kge++ v++k v++ ++l+ lcl|NCBI__GCF_000007065.1:WP_015411247.1 76 LKHAGIACIVAKSFARIFFRNAINIGLPLMEAD--IECE-EGDQIEVDLLKGEVK-VSGKGVFRGNKLP 140 ******************************999..8887.7*************9.9************ PP TIGR02087 139 dllleileeGGlleylkk 156 d+ll++l++GGl+ ++kk lcl|NCBI__GCF_000007065.1:WP_015411247.1 141 DFLLDMLTDGGLVAHRKK 158 ****************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (157 nodes) Target sequences: 1 (168 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.66 // [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