Align 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_034994067.1 DL88_RS07250 3-isopropylmalate dehydratase small subunit
Query= SwissProt::Q1MA52 (202 letters) >NCBI__GCF_000745425.1:WP_034994067.1 Length = 201 Score = 325 bits (833), Expect = 3e-94 Identities = 154/200 (77%), Positives = 170/200 (85%) Query: 1 MDKFVKLTGVAAPLPVVNVDTDMIIPKDYLKTIKRTGLGTGLFAEARYNEDGSENPDFVL 60 MDKF LTGVAAPL + NVDTDMIIPK YLKTIKRTGLG GLF++ R+ EDGSENP+FVL Sbjct: 1 MDKFTTLTGVAAPLKITNVDTDMIIPKQYLKTIKRTGLGEGLFSDLRFKEDGSENPEFVL 60 Query: 61 NKPAYRDAKILVAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIK 120 NKPAYR+A IL+AGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIK Sbjct: 61 NKPAYRNASILIAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIK 120 Query: 121 VSQEDLDKLMDDASRGSNAILTVDLENLEITGPDGGLIKFDLDEFKRHCLLNGLDDIGLT 180 V+ E L L DDA RGSNA LTVDLEN I GPDGG I F++D F++HCLLNGLDDIGLT Sbjct: 121 VTAEQLALLFDDAERGSNATLTVDLENQTIKGPDGGAIHFEIDPFRKHCLLNGLDDIGLT 180 Query: 181 LEKGKAIDSFEKKNAASHPW 200 +EK AI ++E + A H W Sbjct: 181 MEKADAISTYEARQAKEHAW 200 Lambda K H 0.319 0.140 0.419 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: 219 Number of extensions: 4 Number of successful extensions: 1 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: 202 Length of database: 201 Length adjustment: 21 Effective length of query: 181 Effective length of database: 180 Effective search space: 32580 Effective search space used: 32580 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 (21.7 bits) S2: 45 (21.9 bits)
Align candidate WP_034994067.1 DL88_RS07250 (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.4123.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-83 265.5 0.0 1.5e-83 265.3 0.0 1.0 1 lcl|NCBI__GCF_000745425.1:WP_034994067.1 DL88_RS07250 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745425.1:WP_034994067.1 DL88_RS07250 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.3 0.0 1.5e-83 1.5e-83 1 188 [] 1 187 [. 1 187 [. 0.97 Alignments for each domain: == domain 1 score: 265.3 bits; conditional E-value: 1.5e-83 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqg 69 m++f +ltG+++pl+ nvdtd iipkq+lk+ikrtG+g+ lf + r+ e+G ++npefvln p y++ lcl|NCBI__GCF_000745425.1:WP_034994067.1 1 MDKFTTLTGVAAPLKITNVDTDMIIPKQYLKTIKRTGLGEGLFSDLRF-KEDG-SENPEFVLNKPAYRN 67 889*********************************************.5667.79************* PP TIGR00171 70 asillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvk.n 137 asil+a++nfGcGssrehapwal d+G++ +i+ sfadifynn+fkng+lpi+++ e++ l+ + lcl|NCBI__GCF_000745425.1:WP_034994067.1 68 ASILIAGDNFGCGSSREHAPWALLDFGIRCVISTSFADIFYNNCFKNGILPIKVTAEQLALLFDDAErG 136 ****************************************************************99977 PP TIGR00171 138 kglkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkedei 188 + ltvdle+q++k +g ++feid+frkhcllnGld+iglt+ k d+i lcl|NCBI__GCF_000745425.1:WP_034994067.1 137 SNATLTVDLENQTIKGPDGGAIHFEIDPFRKHCLLNGLDDIGLTMEKADAI 187 8899*******************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (201 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: 6.05 // [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