Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_037572526.1 BS73_RS14595 3-isopropylmalate dehydratase large subunit
Query= SwissProt::Q7TXH6 (473 letters) >NCBI__GCF_000744815.1:WP_037572526.1 Length = 474 Score = 743 bits (1917), Expect = 0.0 Identities = 357/465 (76%), Positives = 407/465 (87%), Gaps = 1/465 (0%) Query: 9 RTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELTLATE 68 RTLAEK+WDDH+V G PDL++IDLHL+HEVTSPQAFDGLRLAGR+VRR +LT+ATE Sbjct: 3 RTLAEKVWDDHVVRRVDG-EPDLLFIDLHLLHEVTSPQAFDGLRLAGRKVRRTDLTIATE 61 Query: 69 DHNVPTVDIDQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGPQLGLTQPG 128 DHN PT+DID+PIADPVSRTQ+ETLR+NCAEFG+RLH +GD+EQG+VHVVGPQLGLTQPG Sbjct: 62 DHNTPTLDIDKPIADPVSRTQLETLRKNCAEFGVRLHPLGDVEQGVVHVVGPQLGLTQPG 121 Query: 129 MTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGRLPDGVSAK 188 T+VCGDSHTSTHGAFGALA GIGTS+VEHVLATQTLP+ PFKTMAV V+G LP+GV+AK Sbjct: 122 TTVVCGDSHTSTHGAFGALAFGIGTSQVEHVLATQTLPMAPFKTMAVTVEGELPEGVTAK 181 Query: 189 DIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMVAPDETTYA 248 D+ILA+IA+IGTGGGQG+VIEYRGSA+E LSME RMT+CNMSIEAGARAGM+APDETT+A Sbjct: 182 DLILAVIARIGTGGGQGYVIEYRGSAVEKLSMEARMTVCNMSIEAGARAGMIAPDETTFA 241 Query: 249 FLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTNPGQGVPLA 308 +L+GRPHAP G WD A+ YW+ LRTD AVFD EV +DAA LSPFVTWGTNPGQG PL Sbjct: 242 YLKGRPHAPAGEDWDAAVAYWKTLRTDEDAVFDHEVVIDAAELSPFVTWGTNPGQGAPLG 301 Query: 309 AAVPDPQLMTDDAERQAAEKALAYMDLRPGTAMREIAVDAVFVGSCTNGRIEDLRVVAEV 368 A+VPDP D +ER AAE AL YM L GT +RE+ VDAVFVGSCTNGRIEDLR AEV Sbjct: 302 ASVPDPADYADPSERVAAENALKYMGLTAGTPLREVEVDAVFVGSCTNGRIEDLRAAAEV 361 Query: 369 LRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGMNPDQLASG 428 L+ R++AD VRML+VPGS+RV QA EGL ++FT AGA+WR AGCSMCLGMNPDQLA G Sbjct: 362 LKDRQIADDVRMLVVPGSVRVALQAVEEGLDKVFTAAGAEWRHAGCSMCLGMNPDQLAPG 421 Query: 429 ERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLSSPADLN 473 ERCA+TSNRNFEGRQG GGRTHLVSP VAAATAV G L+SPADL+ Sbjct: 422 ERCASTSNRNFEGRQGKGGRTHLVSPQVAAATAVLGHLASPADLS 466 Lambda K H 0.319 0.135 0.402 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: 814 Number of extensions: 23 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: 473 Length of database: 474 Length adjustment: 33 Effective length of query: 440 Effective length of database: 441 Effective search space: 194040 Effective search space used: 194040 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 (21.8 bits) S2: 51 (24.3 bits)
Align candidate WP_037572526.1 BS73_RS14595 (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.2880919.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-229 748.6 0.0 1.3e-229 748.4 0.0 1.0 1 NCBI__GCF_000744815.1:WP_037572526.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037572526.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 748.4 0.0 1.3e-229 1.3e-229 1 461 [. 1 460 [. 1 465 [. 0.99 Alignments for each domain: == domain 1 score: 748.4 bits; conditional E-value: 1.3e-229 TIGR00170 1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 m +tl ek++d hvv++ ++e+dll+id+hl+hevtspqaf+glr agrkvrr+d t+at dhn +t d NCBI__GCF_000744815.1:WP_037572526.1 1 MGRTLAEKVWDDHVVRRVDGEPDLLFIDLHLLHEVTSPQAFDGLRLAGRKVRRTDLTIATEDHNTPTLDIDKP 73 789********************************************************************** PP TIGR00170 74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146 i + +++ q+++l kn+ efgv+l+ l ++eqg+vhvvgp+ glt pg+t+vcgdsht+thgafgalafgigt NCBI__GCF_000744815.1:WP_037572526.1 74 IADPVSRTQLETLRKNCAEFGVRLHPLGDVEQGVVHVVGPQLGLTQPGTTVVCGDSHTSTHGAFGALAFGIGT 146 ************************************************************************* PP TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219 s+vehvlatqtl a kt+ ++veg+l +g+takd+ila+i +ig+ gg gyv+e+ g a+++lsme+rmtv NCBI__GCF_000744815.1:WP_037572526.1 147 SQVEHVLATQTLPMAPFKTMAVTVEGELPEGVTAKDLILAVIARIGTGGGQGYVIEYRGSAVEKLSMEARMTV 219 ************************************************************************* PP TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292 cnm+ieaga+ag+iapdettf+y+k+r++ap g++++ avaywktl+tde+a+fd++v+++a ++sp vtwgt NCBI__GCF_000744815.1:WP_037572526.1 220 CNMSIEAGARAGMIAPDETTFAYLKGRPHAPAGEDWDAAVAYWKTLRTDEDAVFDHEVVIDAAELSPFVTWGT 292 ************************************************************************* PP TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365 npgq ++ +vpdp++ adp e+ ae+al+y+gl++gt+l++++vd vf+gsctn+riedlraaaev+k + NCBI__GCF_000744815.1:WP_037572526.1 293 NPGQGAPLGASVPDPADYADPSERVAAENALKYMGLTAGTPLREVEVDAVFVGSCTNGRIEDLRAAAEVLKDR 365 ************************************************************************* PP TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438 ++ad+v+ +lvvpgs v qa +egldk+f +ag+ewr+agcs+clgmn+d+l ++ercastsnrnfegrqg NCBI__GCF_000744815.1:WP_037572526.1 366 QIADDVR-MLVVPGSVRVALQAVEEGLDKVFTAAGAEWRHAGCSMCLGMNPDQLAPGERCASTSNRNFEGRQG 437 *******.9**************************************************************** PP TIGR00170 439 kgarthlvspamaaaaavagkfv 461 kg+rthlvsp +aaa+av g+++ NCBI__GCF_000744815.1:WP_037572526.1 438 KGGRTHLVSPQVAAATAVLGHLA 460 *********************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (474 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 24.00 // [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