Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate WP_057509303.1 ABB28_RS14500 3-isopropylmalate dehydratase large subunit
Query= SwissProt::Q7TXH6 (473 letters) >NCBI__GCF_001431535.1:WP_057509303.1 Length = 472 Score = 514 bits (1325), Expect = e-150 Identities = 264/472 (55%), Positives = 321/472 (68%), Gaps = 11/472 (2%) Query: 5 TGEPRTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELT 64 T P TL +K+WD H+VV AP ++YIDLHL+HEVTSPQAF LR G RRP+ T Sbjct: 2 TPAPSTLYDKLWDAHVVVPESDSAPAVLYIDLHLIHEVTSPQAFTELRERGLSPRRPDRT 61 Query: 65 LATEDHNVPTV----DIDQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGP 120 T DH+ PT+ D P A S QV L NCAE+G+ L M ++GIVHV+ P Sbjct: 62 KGTMDHSTPTLPARADGSLPYASAASEAQVAMLASNCAEYGVELFDMASADRGIVHVIAP 121 Query: 121 QLGLTQPGMTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGR 180 + G T PGMTIVCGDSHTSTHGAFG+LA GIGTSEV HVLATQ L R KTMA+ VDG Sbjct: 122 EQGFTLPGMTIVCGDSHTSTHGAFGSLAFGIGTSEVGHVLATQCLLQRKAKTMAITVDGV 181 Query: 181 LPDGVSAKDIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMV 240 LP GV AKD++L +I IG GG GHV+E+RGS I ++ ME RMT+CNMSIEAGARAGMV Sbjct: 182 LPAGVGAKDVVLHIIGVIGVNGGTGHVLEFRGSTIAAMDMEQRMTLCNMSIEAGARAGMV 241 Query: 241 APDETTYAFLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTN 300 APD+ T+ ++ P P GA +D A+ W +LR+D GA FD EV +DAA + P +TWGT+ Sbjct: 242 APDQVTFDWVAATPRGPKGADFDAAVGRWTQLRSDDGARFDAEVTIDAADIRPTLTWGTH 301 Query: 301 PGQGVPLAAAVPDPQLMTDDAERQAAEKALAYMDLRPGTAMREIAVDAVFVGSCTNGRIE 360 PG + + A +P A AA+K L YM L G ++ VD VFVGSCTNGR+ Sbjct: 302 PGTAIAVDAPIP-------AANDAAAQKGLDYMQLHAGDTLQGTPVDVVFVGSCTNGRLS 354 Query: 361 DLRVVAEVLRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGM 420 D+R VA+VL GR+VAD VRML+VPGS V+ QAEAEG+ I AGA+WR+ GCSMC+ M Sbjct: 355 DMREVAQVLHGRQVADRVRMLVVPGSEIVKRQAEAEGIDAIVRAAGAEWREPGCSMCIAM 414 Query: 421 NPDQLASGERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLSSPADL 472 N D +A G+ +TSNRNFEGRQG G RT L SP AA AV G +S DL Sbjct: 415 NGDLVAPGQLAVSTSNRNFEGRQGPGSRTLLASPMTAAWAAVNGRVSDTRDL 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: 718 Number of extensions: 29 Number of successful extensions: 4 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: 472 Length adjustment: 33 Effective length of query: 440 Effective length of database: 439 Effective search space: 193160 Effective search space used: 193160 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_057509303.1 ABB28_RS14500 (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.29816.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-197 640.1 0.1 1.1e-196 639.9 0.1 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509303.1 ABB28_RS14500 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057509303.1 ABB28_RS14500 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 639.9 0.1 1.1e-196 1.1e-196 2 466 .] 5 466 .. 4 466 .. 0.97 Alignments for each domain: == domain 1 score: 639.9 bits; conditional E-value: 1.1e-196 TIGR00170 2 aktlyeklfdahvvk.eaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes 69 + tly+kl+dahvv e+++ + +lyid+hl+hevtspqaf lr++g rr+d+t +t+dh+ +t lcl|NCBI__GCF_001431535.1:WP_057509303.1 5 PSTLYDKLWDAHVVVpESDSAPAVLYIDLHLIHEVTSPQAFTELRERGLSPRRPDRTKGTMDHSTPTLP 73 78**********97627788899*******************************************975 PP TIGR00170 70 r....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtath 134 + + qv l n+ e+gv+lfd+ sa++givhv+ pe+g+tlpg+tivcgdsht+th lcl|NCBI__GCF_001431535.1:WP_057509303.1 74 AradgSLPYASAASEAQVAMLASNCAEYGVELFDMASADRGIVHVIAPEQGFTLPGMTIVCGDSHTSTH 142 54655577889999******************************************************* PP TIGR00170 135 gafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvef 203 gafg+lafgigtsev hvlatq l q +akt+ i+v+g l g+ akd++l iig igv+ggtg+v+ef lcl|NCBI__GCF_001431535.1:WP_057509303.1 143 GAFGSLAFGIGTSEVGHVLATQCLLQRKAKTMAITVDGVLPAGVGAKDVVLHIIGVIGVNGGTGHVLEF 211 ********************************************************************* PP TIGR00170 204 ageairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegak 272 g +i ++ me+rmt+cnm+ieaga+ag++apd++tf++v + pkg++f+ av w l++d+ga+ lcl|NCBI__GCF_001431535.1:WP_057509303.1 212 RGSTIAAMDMEQRMTLCNMSIEAGARAGMVAPDQVTFDWVAATPRGPKGADFDAAVGRWTQLRSDDGAR 280 ********************************************************************* PP TIGR00170 273 fdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdk 341 fd +vt++a di p++twgt pg++++v+ +p+ ++ a a+k l+y+ l++g l+ vd lcl|NCBI__GCF_001431535.1:WP_057509303.1 281 FDAEVTIDAADIRPTLTWGTHPGTAIAVDAPIPAAND-------AAAQKGLDYMQLHAGDTLQGTPVDV 342 *********************************9765.......55789******************** PP TIGR00170 342 vfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcsl 410 vf+gsctn+r+ d+r+ a+v++g++vad v+ +lvvpgs+ vk+qae+eg+d i +ag+ewre+gcs+ lcl|NCBI__GCF_001431535.1:WP_057509303.1 343 VFVGSCTNGRLSDMREVAQVLHGRQVADRVR-MLVVPGSEIVKRQAEAEGIDAIVRAAGAEWREPGCSM 410 *******************************.9************************************ PP TIGR00170 411 clgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466 c++mn d + +++ stsnrnfegrqg g+rt l sp aa aav+g+ d r+l lcl|NCBI__GCF_001431535.1:WP_057509303.1 411 CIAMNGDLVAPGQLAVSTSNRNFEGRQGPGSRTLLASPMTAAWAAVNGRVSDTRDL 466 *****************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (472 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 7.29 // [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