Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_011427156.1 RHE_RS20270 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_000092045.1:WP_011427156.1 Length = 469 Score = 622 bits (1604), Expect = 0.0 Identities = 305/462 (66%), Positives = 368/462 (79%), Gaps = 1/462 (0%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 +TLY+K++D H+V E + T LLYIDRHLVHEVTSPQAF+GLR GR VR P KT A +D Sbjct: 5 RTLYDKIWDDHLVDEQADGTCLLYIDRHLVHEVTSPQAFEGLRMSGRKVRAPEKTLAVVD 64 Query: 63 HNVSTQT-KDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPG 121 HNV T + + E +RIQ+++L KN EF VE Y N QGIVH++GPEQG TLPG Sbjct: 65 HNVPTSPDRHLGIKNEESRIQVEQLAKNAAEFNVEYYSENDKRQGIVHIIGPEQGFTLPG 124 Query: 122 MTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAK 181 MTIVCGDSHT+THGAFG+LA GIGTSEVEHVLATQTL Q +AK M ++V G+ G+TAK Sbjct: 125 MTIVCGDSHTSTHGAFGSLAHGIGTSEVEHVLATQTLIQKKAKNMLVQVDGQLPAGVTAK 184 Query: 182 DIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFN 241 DIVLAIIG+ G+AGGTG+V+E+ GEAIR LSMEGRMT+CNM+IE GA+AGL+APDE TF Sbjct: 185 DIVLAIIGEIGTAGGTGYVIEYAGEAIRSLSMEGRMTICNMSIEGGARAGLIAPDEITFE 244 Query: 242 YVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVN 301 Y+KG+ APKG+ + A+AYWKTL++DEGA FD +V L A E+ P V+WG++P V+SV Sbjct: 245 YIKGKPRAPKGEALEQAIAYWKTLKSDEGAHFDRIVKLNAAELPPIVSWGSSPEDVVSVQ 304 Query: 302 DNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEI 361 +P+P D +RAS +AL YMGLKPG +T++A+D+VFIGSCTN RIEDLRAAA++ Sbjct: 305 GIVPNPDEIQDETKRASKWRALDYMGLKPGTKMTDIAVDRVFIGSCTNGRIEDLRAAAKV 364 Query: 362 AKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421 +G+ VA V A++VPGSG VK QAEAEGLDKIF AGF+WR PGCSMCLAMN+DRL PG Sbjct: 365 VEGKTVASTVNAMIVPGSGLVKEQAEAEGLDKIFKAAGFDWREPGCSMCLAMNDDRLKPG 424 Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463 ERCASTSNRNFEGRQG GRTHLVSP MAAAAA+ GHF DIR Sbjct: 425 ERCASTSNRNFEGRQGFKGRTHLVSPTMAAAAAIAGHFVDIR 466 Lambda K H 0.317 0.134 0.396 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: 777 Number of extensions: 25 Number of successful extensions: 2 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: 466 Length of database: 469 Length adjustment: 33 Effective length of query: 433 Effective length of database: 436 Effective search space: 188788 Effective search space used: 188788 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_011427156.1 RHE_RS20270 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large 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/TIGR00170.hmm # target sequence database: /tmp/gapView.5731.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00170 [M=466] Accession: TIGR00170 Description: leuC: 3-isopropylmalate dehydratase, large 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-247 806.7 0.1 3.2e-247 806.5 0.1 1.0 1 lcl|NCBI__GCF_000092045.1:WP_011427156.1 RHE_RS20270 3-isopropylmalate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092045.1:WP_011427156.1 RHE_RS20270 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 806.5 0.1 3.2e-247 3.2e-247 2 465 .. 4 467 .. 3 468 .. 0.99 Alignments for each domain: == domain 1 score: 806.5 bits; conditional E-value: 3.2e-247 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhniste.s 69 ++tly+k++d h+v e+ ++t llyidrhlvhevtspqafeglr grkvr ++ktla +dhn++t lcl|NCBI__GCF_000092045.1:WP_011427156.1 4 PRTLYDKIWDDHLVDEQADGTCLLYIDRHLVHEVTSPQAFEGLRMSGRKVRAPEKTLAVVDHNVPTSpD 72 8*****************************************************************846 PP TIGR00170 70 rdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafg 138 r + ik+e++++qv++l kn+ ef v+++ ++++qgivh++gpe+g+tlpg+tivcgdsht+thgafg lcl|NCBI__GCF_000092045.1:WP_011427156.1 73 RHLGIKNEESRIQVEQLAKNAAEFNVEYYSENDKRQGIVHIIGPEQGFTLPGMTIVCGDSHTSTHGAFG 141 89******************************************************************* PP TIGR00170 139 alafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefagea 207 +la gigtsevehvlatqtl+q++ak++ ++v+g+l g+takdi+laiig ig+aggtgyv+e+agea lcl|NCBI__GCF_000092045.1:WP_011427156.1 142 SLAHGIGTSEVEHVLATQTLIQKKAKNMLVQVDGQLPAGVTAKDIVLAIIGEIGTAGGTGYVIEYAGEA 210 ********************************************************************* PP TIGR00170 208 irdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkv 276 ir+lsme+rmt+cnm+ie ga+agliapde+tfey+k+++ apkg+ e+a+aywktlk+dega+fd+ lcl|NCBI__GCF_000092045.1:WP_011427156.1 211 IRSLSMEGRMTICNMSIEGGARAGLIAPDEITFEYIKGKPRAPKGEALEQAIAYWKTLKSDEGAHFDRI 279 ********************************************************************* PP TIGR00170 277 vtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfig 345 v+l+a ++ p v+wg +p++v+sv++ vp+p+++ d+ ++as +al+y+gl+pgtk++di+vd+vfig lcl|NCBI__GCF_000092045.1:WP_011427156.1 280 VKLNAAELPPIVSWGSSPEDVVSVQGIVPNPDEIQDETKRASKWRALDYMGLKPGTKMTDIAVDRVFIG 348 ********************************************************************* PP TIGR00170 346 sctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgm 414 sctn+riedlraaa+vv gk va++v+ a++vpgsglvk+qae+egldkif +agf+wre+gcs+cl+m lcl|NCBI__GCF_000092045.1:WP_011427156.1 349 SCTNGRIEDLRAAAKVVEGKTVASTVN-AMIVPGSGLVKEQAEAEGLDKIFKAAGFDWREPGCSMCLAM 416 ***************************.***************************************** PP TIGR00170 415 nndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465 n+d+l+++ercastsnrnfegrqg ++rthlvsp+maaaaa+ag+fvdire lcl|NCBI__GCF_000092045.1:WP_011427156.1 417 NDDRLKPGERCASTSNRNFEGRQGFKGRTHLVSPTMAAAAAIAGHFVDIRE 467 **************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (469 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: 00:00:00.01 # Mc/sec: 10.94 // [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