Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_011386418.1 AMB_RS20560 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_000009985.1:WP_011386418.1 Length = 467 Score = 623 bits (1607), Expect = 0.0 Identities = 310/463 (66%), Positives = 364/463 (78%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 +TL++K++DAH+V ++ T L+YIDRH+VHEVTSPQAF+GL GR VR P T A D Sbjct: 5 RTLFDKIWDAHLVDVQDDGTCLIYIDRHMVHEVTSPQAFEGLEMSGRKVRHPELTLAVAD 64 Query: 63 HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122 HNV T + E +RIQ++ L N K+FGVE ++ QG+VH++GPEQG TLPG Sbjct: 65 HNVPTTDRSKGIENEESRIQVETLEANAKKFGVEYLRMDDIRQGVVHIVGPEQGFTLPGT 124 Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182 TIVCGDSHTATHGAFG+LAFGIGTSEVEHVLATQTL Q AK M+I V GK PG+TAKD Sbjct: 125 TIVCGDSHTATHGAFGSLAFGIGTSEVEHVLATQTLVQKPAKNMRITVTGKPGPGVTAKD 184 Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242 IVLAIIGK G+AGGTG+VVEF GEAIRDLSMEGRMT+CNM IE GA+AGLVAPDE TF Y Sbjct: 185 IVLAIIGKIGTAGGTGYVVEFAGEAIRDLSMEGRMTVCNMTIEAGARAGLVAPDEKTFAY 244 Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302 + G+ +PKG F+ AV+YWKTL TDEGA FD VTL A + PQ+TWGT+P VI++ Sbjct: 245 IAGKPRSPKGAAFEAAVSYWKTLFTDEGAHFDAEVTLDASTLVPQITWGTSPEDVIAITG 304 Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362 +P+PA D +R + E++L YMGL G+ T++AID VFIGSCTN RIED RAAAEI Sbjct: 305 TVPNPADIKDEAKRKAVERSLDYMGLTAGMKATDIAIDVVFIGSCTNGRIEDFRAAAEIF 364 Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422 KGRKVA VQAL+VPGSG VK QAE EGLDKIFIEAG EWR PGCSMCLAMN D+L PG+ Sbjct: 365 KGRKVAASVQALIVPGSGLVKEQAEQEGLDKIFIEAGAEWREPGCSMCLAMNADQLKPGQ 424 Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 R ASTSNRNFEGRQGRGGRTHLVSPAMAAAAA+TG D+R++ Sbjct: 425 RSASTSNRNFEGRQGRGGRTHLVSPAMAAAAAITGKLTDVRSL 467 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: 760 Number of extensions: 27 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: 466 Length of database: 467 Length adjustment: 33 Effective length of query: 433 Effective length of database: 434 Effective search space: 187922 Effective search space used: 187922 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_011386418.1 AMB_RS20560 (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.15048.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-243 793.8 1.7 2.8e-243 793.5 1.7 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386418.1 AMB_RS20560 3-isopropylmalate de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386418.1 AMB_RS20560 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 793.5 1.7 2.8e-243 2.8e-243 3 465 .. 5 466 .. 3 467 .] 1.00 Alignments for each domain: == domain 1 score: 793.5 bits; conditional E-value: 2.8e-243 TIGR00170 3 ktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrd 71 +tl++k++dah+v ++++t l+yidrh+vhevtspqafegl+ grkvr+++ tla dhn++t+ r lcl|NCBI__GCF_000009985.1:WP_011386418.1 5 RTLFDKIWDAHLVDVQDDGTCLIYIDRHMVHEVTSPQAFEGLEMSGRKVRHPELTLAVADHNVPTTDRS 73 8******************************************************************** PP TIGR00170 72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgal 140 i +e++++qv++le n+k+fgv+++ +++ +qg+vh+vgpe+g+tlpg+tivcgdshtathgafg+l lcl|NCBI__GCF_000009985.1:WP_011386418.1 74 KGIENEESRIQVETLEANAKKFGVEYLRMDDIRQGVVHIVGPEQGFTLPGTTIVCGDSHTATHGAFGSL 142 ********************************************************************* PP TIGR00170 141 afgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageair 209 afgigtsevehvlatqtl+q+ ak+++i+v gk +g+takdi+laiigkig+aggtgyvvefageair lcl|NCBI__GCF_000009985.1:WP_011386418.1 143 AFGIGTSEVEHVLATQTLVQKPAKNMRITVTGKPGPGVTAKDIVLAIIGKIGTAGGTGYVVEFAGEAIR 211 ********************************************************************* PP TIGR00170 210 dlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvt 278 dlsme+rmtvcnm+ieaga+agl+apde tf+y+ +++ +pkg+ fe av+ywktl tdega+fd +vt lcl|NCBI__GCF_000009985.1:WP_011386418.1 212 DLSMEGRMTVCNMTIEAGARAGLVAPDEKTFAYIAGKPRSPKGAAFEAAVSYWKTLFTDEGAHFDAEVT 280 ********************************************************************* PP TIGR00170 279 leakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsc 347 l+a+ ++pq+twgt+p++v++++++vp+p+++ d+ +++ +e++l+y+gl++g+k +di++d vfigsc lcl|NCBI__GCF_000009985.1:WP_011386418.1 281 LDASTLVPQITWGTSPEDVIAITGTVPNPADIKDEAKRKAVERSLDYMGLTAGMKATDIAIDVVFIGSC 349 ********************************************************************* PP TIGR00170 348 tnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnn 416 tn+ried+raaae+ kg+kva +v+ al+vpgsglvk+qae+egldkif+eag+ewre+gcs+cl+mn lcl|NCBI__GCF_000009985.1:WP_011386418.1 350 TNGRIEDFRAAAEIFKGRKVAASVQ-ALIVPGSGLVKEQAEQEGLDKIFIEAGAEWREPGCSMCLAMNA 417 *************************.******************************************* PP TIGR00170 417 dvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465 d+l++++r astsnrnfegrqg+g+rthlvspamaaaaa++gk+ d+r lcl|NCBI__GCF_000009985.1:WP_011386418.1 418 DQLKPGQRSASTSNRNFEGRQGRGGRTHLVSPAMAAAAAITGKLTDVRS 466 ***********************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (467 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: 10.98 // [ok]
This GapMind analysis is from Apr 09 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