Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_059152441.1 V474_RS16025 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_001046635.1:WP_059152441.1 Length = 479 Score = 559 bits (1441), Expect = e-164 Identities = 281/470 (59%), Positives = 355/470 (75%), Gaps = 7/470 (1%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 +TLY+K++DAHVV ++ T L+YIDRH+VHEVTSPQAF+ LRA GRPVR+P T A D Sbjct: 6 RTLYQKIWDAHVVDTRDDGTCLIYIDRHIVHEVTSPQAFESLRAAGRPVRRPDLTLAVPD 65 Query: 63 HNV-STQTKDINA----CGEMARIQMQELI-KNCKEFGVELYDLNHPYQGIVHVMGPEQG 116 HN+ +T +D N ++ Q +L+ KN FG+ QGIVHV+GPEQG Sbjct: 66 HNLPTTARRDANGNRIPIADLQSAQQLDLLEKNAPAFGIRYIGDADREQGIVHVVGPEQG 125 Query: 117 VTLPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAP 176 +LPG TIVCGDSHTA +G GALAFGIGTSEVEHVLATQTL ++KT ++ V+G Sbjct: 126 FSLPGATIVCGDSHTACNGGLGALAFGIGTSEVEHVLATQTLLLKQSKTFEVRVEGTLGA 185 Query: 177 GITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD 236 G+T KD++L IIG G+AGGTG+V+E+ G R++S+EGR+T+ NM+IE GA+AGLVAPD Sbjct: 186 GVTPKDVILHIIGLIGTAGGTGYVIEYTGNVFREMSVEGRLTVSNMSIEGGARAGLVAPD 245 Query: 237 ETTFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQ 296 + TF+YVKGR +APKG+++D AVA+WK+L TDEGAT+D V ++AE+I P +TWGT+P Sbjct: 246 DITFDYVKGRPYAPKGEEWDKAVAWWKSLATDEGATYDKSVFIRAEDIQPTITWGTSPED 305 Query: 297 VISVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLR 356 ++ +P P FAD +R + + +L YMGL PG+ LTEV + VFIGSCTNSRIED+R Sbjct: 306 TSAIGGVVPAPEDFADASKRDAVKHSLEYMGLTPGMKLTEVEVQNVFIGSCTNSRIEDIR 365 Query: 357 AAAEIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNN 415 AAAE+ KGR A V+ A+VVPGSG VK QAEAEGLDKI I+AG EWR PGCS CLAMN Sbjct: 366 AAAEVLKGRHKADNVKWAIVVPGSGLVKEQAEAEGLDKIIIDAGLEWREPGCSACLAMNP 425 Query: 416 DRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465 D++ PGERCASTSNRNF GRQG G RTHL+SPAMAAAAAVTG D+R++ Sbjct: 426 DKVPPGERCASTSNRNFTGRQGPGARTHLMSPAMAAAAAVTGKLTDVRDL 475 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: 755 Number of extensions: 18 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: 479 Length adjustment: 33 Effective length of query: 433 Effective length of database: 446 Effective search space: 193118 Effective search space used: 193118 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_059152441.1 V474_RS16025 (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.1306602.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-229 745.8 0.0 9.3e-229 745.6 0.0 1.0 1 NCBI__GCF_001046635.1:WP_059152441.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001046635.1:WP_059152441.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 745.6 0.0 9.3e-229 9.3e-229 2 466 .] 5 475 .. 4 475 .. 0.99 Alignments for each domain: == domain 1 score: 745.6 bits; conditional E-value: 9.3e-229 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr.... 70 ++tly+k++dahvv +++t l+yidrh+vhevtspqafe lraagr+vrr+d tla dhn++t++r NCBI__GCF_001046635.1:WP_059152441.1 5 PRTLYQKIWDAHVVDTRDDGTCLIYIDRHIVHEVTSPQAFESLRAAGRPVRRPDLTLAVPDHNLPTTARrdan 77 8*****************************************************************9998887 PP TIGR00170 71 ..dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgala 141 + i + ++ q+ lekn+ +fg+++++ + eqgivhvvgpe+g++lpg tivcgdshta g +gala NCBI__GCF_001046635.1:WP_059152441.1 78 gnRIPIADLQSAQQLDLLEKNAPAFGIRYIGDADREQGIVHVVGPEQGFSLPGATIVCGDSHTACNGGLGALA 150 7778899****************************************************************** PP TIGR00170 142 fgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsme 214 fgigtsevehvlatqtl +++kt++++veg+l g+t kd+il iig+ig+aggtgyv+e++g+++r++s+e NCBI__GCF_001046635.1:WP_059152441.1 151 FGIGTSEVEHVLATQTLLLKQSKTFEVRVEGTLGAGVTPKDVILHIIGLIGTAGGTGYVIEYTGNVFREMSVE 223 ************************************************************************* PP TIGR00170 215 ermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispq 287 +r+tv nm+ie ga+agl+apd++tf+yvk+r+yapkg+e++kava wk+l tdega++dk+v + a+di p+ NCBI__GCF_001046635.1:WP_059152441.1 224 GRLTVSNMSIEGGARAGLVAPDDITFDYVKGRPYAPKGEEWDKAVAWWKSLATDEGATYDKSVFIRAEDIQPT 296 ************************************************************************* PP TIGR00170 288 vtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaae 360 +twgt+p++ ++ + vp+p+++ad ++ ++++l+y+gl+pg+kl++++v++vfigsctnsried+raaae NCBI__GCF_001046635.1:WP_059152441.1 297 ITWGTSPEDTSAIGGVVPAPEDFADASKRDAVKHSLEYMGLTPGMKLTEVEVQNVFIGSCTNSRIEDIRAAAE 369 ************************************************************************* PP TIGR00170 361 vvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnf 433 v+kg+++adnvk a+vvpgsglvk+qae+egldki+++ag+ewre+gcs cl+mn+d+++++ercastsnrnf NCBI__GCF_001046635.1:WP_059152441.1 370 VLKGRHKADNVKWAIVVPGSGLVKEQAEAEGLDKIIIDAGLEWREPGCSACLAMNPDKVPPGERCASTSNRNF 442 ************************************************************************* PP TIGR00170 434 egrqgkgarthlvspamaaaaavagkfvdirel 466 grqg garthl+spamaaaaav+gk+ d+r+l NCBI__GCF_001046635.1:WP_059152441.1 443 TGRQGPGARTHLMSPAMAAAAAVTGKLTDVRDL 475 *******************************85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (479 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 29.05 // [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