Align 3-isopropylmalate dehydratase subunit LeuD (EC 4.2.1.33) (characterized)
to candidate WP_086508302.1 BZY95_RS01835 3-isopropylmalate dehydratase small subunit
Query= ecocyc::LEUD-MONOMER (201 letters) >NCBI__GCF_002151265.1:WP_086508302.1 Length = 210 Score = 147 bits (372), Expect = 1e-40 Identities = 84/182 (46%), Positives = 111/182 (60%), Gaps = 3/182 (1%) Query: 14 PLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPDFVLNFPQYQGASI 73 PL ANVDTD +IP +F+++ G+G L +D R DE G+ P F+LN PQ A Sbjct: 13 PLPLANVDTDQLIPARFMKEPRSVGYGRFLLHDLRH-DENGR-PVVGFILNHPQADEAKT 70 Query: 74 LLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPVKLSDAEVDELF 133 L+AR NFG GSSRE A +AL D+GF+ VIAPSF DIF N+ NN LLP +S+A+ + L Sbjct: 71 LVARRNFGAGSSREAAVYALVDFGFRCVIAPSFGDIFASNAVNNGLLPATVSEADAEALL 130 Query: 134 ALVKANPGIHFDVDLEAQEVKAGEKTYRFTIDAFRRHCMMNGLDSIGLTLQHDDAIAAYE 193 A + +P VDLEAQ + GE + FTI R ++NG D I +T QH IA + Sbjct: 131 AALGESPA-PLRVDLEAQRIAIGELSVAFTIAPTWRTKLLNGWDDIDMTRQHAATIARFA 189 Query: 194 AK 195 + Sbjct: 190 TR 191 Lambda K H 0.322 0.138 0.421 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: 139 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: 201 Length of database: 210 Length adjustment: 21 Effective length of query: 180 Effective length of database: 189 Effective search space: 34020 Effective search space used: 34020 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 (21.9 bits) S2: 45 (21.9 bits)
Align candidate WP_086508302.1 BZY95_RS01835 (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.1404.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-56 175.4 0.0 6.2e-56 175.3 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508302.1 BZY95_RS01835 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508302.1 BZY95_RS01835 3-isopropylmalate dehydratase small subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 175.3 0.0 6.2e-56 6.2e-56 1 187 [. 1 184 [. 1 185 [. 0.97 Alignments for each domain: == domain 1 score: 175.3 bits; conditional E-value: 6.2e-56 TIGR00171 1 mkefkkltGlvvpldkanvdtdaiipkqflkkikrtGfgkhlfyewryldekGkepnpefvlnvpqyqg 69 m+++k + + pl anvdtd++ip +f+k+ + +G+g++l+++ r+ de+G p f+ln+pq + lcl|NCBI__GCF_002151265.1:WP_086508302.1 1 MEPIKIIDAPACPLPLANVDTDQLIPARFMKEPRSVGYGRFLLHDLRH-DENG-RPVVGFILNHPQADE 67 788888899999***********************************9.****.89************* PP TIGR00171 70 asillarenfGcGssrehapwalkdyGfkviiapsfadifynnsfkngllpirlseeeveellalvknk 138 a+ l+ar nfG Gssre a +al d+Gf+ +iapsf+dif +n+++ngllp +se++ e lla + ++ lcl|NCBI__GCF_002151265.1:WP_086508302.1 68 AKTLVARRNFGAGSSREAAVYALVDFGFRCVIAPSFGDIFASNAVNNGLLPATVSEADAEALLAALGES 136 ********************************************************************* PP TIGR00171 139 glkltvdleaqkvkdsegkvysfeidefrkhcllnGldeigltlqkede 187 l vdleaq++ +e + f+i + ++ llnG+d+i +t q+ + lcl|NCBI__GCF_002151265.1:WP_086508302.1 137 PAPLRVDLEAQRIAIGE-LSVAFTIAPTWRTKLLNGWDDIDMTRQHAAT 184 *****************.999***********************99765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (188 nodes) Target sequences: 1 (210 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 7.21 // [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