Align 3-isopropylmalate dehydratase large subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 (characterized)
to candidate N515DRAFT_0572 N515DRAFT_0572 3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit
Query= SwissProt::Q7TXH6 (473 letters) >FitnessBrowser__Dyella79:N515DRAFT_0572 Length = 471 Score = 544 bits (1401), Expect = e-159 Identities = 270/468 (57%), Positives = 339/468 (72%), Gaps = 13/468 (2%) Query: 9 RTLAEKIWDDHIVVSGGGCAPDLIYIDLHLVHEVTSPQAFDGLRLAGRRVRRPELTLATE 68 RTL EK+WD H+V P ++YIDLHLVHEVTSPQAF LR G ++RRP+ LAT Sbjct: 4 RTLFEKLWDAHVVAPETADTPAILYIDLHLVHEVTSPQAFSELRERGLKLRRPDRALATL 63 Query: 69 DHNVPTVDI----DQPIADPVSRTQVETLRRNCAEFGIRLHSMGDIEQGIVHVVGPQLGL 124 DH+ PT+ ++P A+ ++ QV L NC EFG+ LH E+GIVHV+GP+LG Sbjct: 64 DHSTPTLPANDKGERPYANEEAKAQVAQLEANCREFGVELHGWDSSERGIVHVIGPELGA 123 Query: 125 TQPGMTIVCGDSHTSTHGAFGALAMGIGTSEVEHVLATQTLPLRPFKTMAVNVDGRLPDG 184 TQPGMTIVCGDSHTSTHGAFGALA GIGT+EV HV+ATQ L R KT+A++VDG+LP G Sbjct: 124 TQPGMTIVCGDSHTSTHGAFGALAFGIGTTEVGHVMATQCLLQRKPKTLAIHVDGQLPKG 183 Query: 185 VSAKDIILALIAKIGTGGGQGHVIEYRGSAIESLSMEGRMTICNMSIEAGARAGMVAPDE 244 + AKD+IL +I +IG GG GHVIEYRG AIE+LSM+ RMT+CNMSIEAGARAG++APD+ Sbjct: 184 IGAKDLILHIIGEIGVDGGTGHVIEYRGEAIEALSMDERMTVCNMSIEAGARAGLIAPDD 243 Query: 245 TTYAFLRGRPHAPTGAQWDTALVYWQRLRTDVGAVFDTEVYLDAASLSPFVTWGTNPGQG 304 TT+A+L+GRP P GA WD A+ W+ LRTD GA +D EV +DA+ + P VT+GT+PG Sbjct: 244 TTFAWLKGRPRVPQGAAWDAAVAKWRALRTDAGASYDREVRIDASKVKPTVTYGTHPGMA 303 Query: 305 VPLAAAVPDPQLMTDDAERQAAE-KALAYMDLRPGTAMREIAVDAVFVGSCTNGRIEDLR 363 + + A VP A R A E +AL YM +PG M+ VD VF+GSCTN R+ DLR Sbjct: 304 IAMDAPVP--------AARSAQETRALDYMRAQPGKPMQGTPVDVVFIGSCTNSRLSDLR 355 Query: 364 VVAEVLRGRKVADGVRMLIVPGSMRVRAQAEAEGLGEIFTDAGAQWRQAGCSMCLGMNPD 423 A +LRGR++A+GVRML+VPGS VR AE EGL ++FT AGA+WR GCSMC+ MN D Sbjct: 356 EAAAILRGRRIAEGVRMLVVPGSEAVRRDAEREGLHQVFTAAGAEWRVPGCSMCIAMNGD 415 Query: 424 QLASGERCAATSNRNFEGRQGAGGRTHLVSPAVAAATAVRGTLSSPAD 471 G+ +TSNRNFEGRQG G RT L SPA AAA+A+ G+++ P + Sbjct: 416 LAQPGQLVVSTSNRNFEGRQGKGARTVLASPATAAASALAGSIADPRE 463 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: 699 Number of extensions: 26 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: 473 Length of database: 471 Length adjustment: 33 Effective length of query: 440 Effective length of database: 438 Effective search space: 192720 Effective search space used: 192720 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 N515DRAFT_0572 N515DRAFT_0572 (3-isopropylmalate/(R)-2-methylmalate 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.18454.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-202 658.6 0.0 2.8e-202 658.3 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 N515DRAFT_0572 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 N515DRAFT_0572 3-isopropylmalate/(R)-2-methylmalate dehydratase large su # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 658.3 0.0 2.8e-202 2.8e-202 2 465 .. 3 463 .. 2 464 .. 0.97 Alignments for each domain: == domain 1 score: 658.3 bits; conditional E-value: 2.8e-202 TIGR00170 2 aktlyeklfdahvvkeaen.etdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnis 66 a+tl+ekl+dahvv + + + +lyid+hlvhevtspqaf lr++g k+rr+d++latldh+ + lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 3 ARTLFEKLWDAHVVAPETAdTPAILYIDLHLVHEVTSPQAFSELRERGLKLRRPDRALATLDHSTP 68 89************9666505679*****************************************9 PP TIGR00170 67 tesr....dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgd 128 t + +e+ak qv +le n++efgv+l++ +s+e+givhv+gpe g t pg+tivcgd lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 69 TLPAndkgERPYANEEAKAQVAQLEANCREFGVELHGWDSSERGIVHVIGPELGATQPGMTIVCGD 134 97553334566789**************************************************** PP TIGR00170 129 shtathgafgalafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigva 194 sht+thgafgalafgigt+ev hv+atq l q ++ktl i+v+g+l kgi akd+il iig igv lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 135 SHTSTHGAFGALAFGIGTTEVGHVMATQCLLQRKPKTLAIHVDGQLPKGIGAKDLILHIIGEIGVD 200 ****************************************************************** PP TIGR00170 195 ggtgyvvefageairdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekava 260 ggtg+v+e+ geai++lsm+ermtvcnm+ieaga+agliapd+ttf+++k+r+ p+g+ ++ ava lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 201 GGTGHVIEYRGEAIEALSMDERMTVCNMSIEAGARAGLIAPDDTTFAWLKGRPRVPQGAAWDAAVA 266 ****************************************************************** PP TIGR00170 261 ywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalayl 326 +w++l+td ga +d++v ++a+++ p+vt+gt pg++++++ vp+ +s a+ +al+y+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 267 KWRALRTDAGASYDREVRIDASKVKPTVTYGTHPGMAIAMDAPVPAARS-------AQETRALDYM 325 ******************************************9998776.......45679***** PP TIGR00170 327 glepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegl 392 +pg++++ vd vfigsctnsr+ dlr+aa++++g+++a++v+ +lvvpgs++v+++ae+egl lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 326 RAQPGKPMQGTPVDVVFIGSCTNSRLSDLREAAAILRGRRIAEGVR-MLVVPGSEAVRRDAEREGL 390 **********************************************.9****************** PP TIGR00170 393 dkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavag 458 ++f +ag+ewr +gcs+c++mn d ++++ stsnrnfegrqgkgart l spa aaa+a+ag lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 391 HQVFTAAGAEWRVPGCSMCIAMNGDLAQPGQLVVSTSNRNFEGRQGKGARTVLASPATAAASALAG 456 ****************************************************************** PP TIGR00170 459 kfvdire 465 ++d re lcl|FitnessBrowser__Dyella79:N515DRAFT_0572 457 SIADPRE 463 ***9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (471 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: 12.17 // [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