Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_010532011.1 ON01_RS15975 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_000224785.1:WP_010532011.1 Length = 469 Score = 558 bits (1437), Expect = e-163 Identities = 275/461 (59%), Positives = 347/461 (75%), Gaps = 4/461 (0%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 +T+ EK++ H+V++ + L+YID HLVHEVTSPQAF+GLR + R VR+P TFATMD Sbjct: 5 ETIVEKIWKNHLVHKEPEKPNLMYIDLHLVHEVTSPQAFEGLRLNNRKVRRPDLTFATMD 64 Query: 63 HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122 HNV T+ +D+ ++++ QM+ L KNCK+FG+ L D+ HP QGIVHV+GP+ G+T PG Sbjct: 65 HNVPTKNRDVIE-DQISQKQMETLRKNCKDFGITLADMFHPDQGIVHVIGPQLGLTQPGK 123 Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182 TIVCGDSHT+THGAFGALAFGIGTSEVEHVLATQTL Q KT+ + V+G G+TAKD Sbjct: 124 TIVCGDSHTSTHGAFGALAFGIGTSEVEHVLATQTLWQKPPKTLNVHVEGDLGTGVTAKD 183 Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242 ++LAII K G GTG+V+E+ GEAIR+LSMEGRMT+CNM+IE GA+AGL++PDETT + Sbjct: 184 LILAIISKFGVRFGTGYVMEYTGEAIRNLSMEGRMTVCNMSIEAGARAGLISPDETTVEF 243 Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302 ++ + H P+G+ FD+ W L TDEGA +D VT++A+EI PQV+WGTNPG + V+ Sbjct: 244 LRDKPHVPQGEAFDEKAREWLALATDEGAEYDETVTIKADEIEPQVSWGTNPGMCVPVSG 303 Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362 + PD + +AL YMGL+ P+ + ID VFIGSCTNSRI DLR AA++ Sbjct: 304 STPD---VNESDNHDDVARALEYMGLEENQPIQSIDIDHVFIGSCTNSRITDLRKAAKVV 360 Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422 +G +V V+A+VVPGS K QAE EGLD IF EAGFEWR GCSMCLAMN+D + PG Sbjct: 361 EGHQVNDDVRAIVVPGSFGTKLQAEKEGLDAIFKEAGFEWREAGCSMCLAMNDDVVPPGG 420 Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463 RCASTSNRNFEGRQG G RTHLVSP MAAAAA+ GHF D+R Sbjct: 421 RCASTSNRNFEGRQGNGARTHLVSPEMAAAAAIEGHFVDVR 461 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: 753 Number of extensions: 28 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: 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_010532011.1 ON01_RS15975 (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.4130743.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-234 763.7 0.1 3.5e-234 763.5 0.1 1.0 1 NCBI__GCF_000224785.1:WP_010532011.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010532011.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 763.5 0.1 3.5e-234 3.5e-234 2 466 .] 4 463 .. 3 463 .. 0.99 Alignments for each domain: == domain 1 score: 763.5 bits; conditional E-value: 3.5e-234 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdvei 74 + t++ek++ +h+v+++ ++++l+yid+hlvhevtspqafeglr ++rkvrr+d t+at+dhn++t++rdv i NCBI__GCF_000224785.1:WP_010532011.1 4 PETIVEKIWKNHLVHKEPEKPNLMYIDLHLVHEVTSPQAFEGLRLNNRKVRRPDLTFATMDHNVPTKNRDV-I 75 78*******************************************************************98.6 PP TIGR00170 75 keekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigts 147 ++ ++ q+++l kn+k+fg+ l+d+ + +qgivhv+gp+ glt pgktivcgdsht+thgafgalafgigts NCBI__GCF_000224785.1:WP_010532011.1 76 EDQISQKQMETLRKNCKDFGITLADMFHPDQGIVHVIGPQLGLTQPGKTIVCGDSHTSTHGAFGALAFGIGTS 148 78999******************************************************************** PP TIGR00170 148 evehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvc 220 evehvlatqtl+q+ +ktl+++veg l +g+takd+ilaii k gv++gtgyv+e++geair+lsme+rmtvc NCBI__GCF_000224785.1:WP_010532011.1 149 EVEHVLATQTLWQKPPKTLNVHVEGDLGTGVTAKDLILAIISKFGVRFGTGYVMEYTGEAIRNLSMEGRMTVC 221 ************************************************************************* PP TIGR00170 221 nmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtn 293 nm+ieaga+agli+pdett e+++d+++ p+g+ f++ +w +l tdega++d++vt++a++i pqv+wgtn NCBI__GCF_000224785.1:WP_010532011.1 222 NMSIEAGARAGLISPDETTVEFLRDKPHVPQGEAFDEKAREWLALATDEGAEYDETVTIKADEIEPQVSWGTN 294 ************************************************************************* PP TIGR00170 294 pgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkk 366 pg+ ++v+++ pd + + +++ ++ +al+y+gle ++++++i +d+vfigsctnsri+dlr+aa+vv g++ NCBI__GCF_000224785.1:WP_010532011.1 295 PGMCVPVSGSTPDVN---ESDNHDDVARALEYMGLEENQPIQSIDIDHVFIGSCTNSRITDLRKAAKVVEGHQ 364 ************865...566778899********************************************** PP TIGR00170 367 vadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgk 439 v d+v+ a+vvpgs k qaekegld if eagfewreagcs+cl+mn+dv++++ rcastsnrnfegrqg+ NCBI__GCF_000224785.1:WP_010532011.1 365 VNDDVR-AIVVPGSFGTKLQAEKEGLDAIFKEAGFEWREAGCSMCLAMNDDVVPPGGRCASTSNRNFEGRQGN 436 ******.****************************************************************** PP TIGR00170 440 garthlvspamaaaaavagkfvdirel 466 garthlvsp maaaaa+ g+fvd+r++ NCBI__GCF_000224785.1:WP_010532011.1 437 GARTHLVSPEMAAAAAIEGHFVDVRQF 463 *************************86 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: 20.46 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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