Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_106714736.1 CU100_RS01185 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_003010935.1:WP_106714736.1 Length = 469 Score = 614 bits (1584), Expect = e-180 Identities = 307/467 (65%), Positives = 366/467 (78%), Gaps = 5/467 (1%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 +TLY+K++D H+V E+ T LLYIDRHLVHEVTSPQAF+GLR GR VR P KT A +D Sbjct: 5 RTLYDKIWDDHLVDSQEDGTCLLYIDRHLVHEVTSPQAFEGLRLTGRKVRHPEKTLAVVD 64 Query: 63 HNVST---QTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119 HN+ T +TK I +RIQ++ L +N +FGVE Y QGIVH++GPEQG TL Sbjct: 65 HNIPTSPDRTKRIE--NNESRIQVEALARNALDFGVEYYSEKDIRQGIVHIIGPEQGFTL 122 Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179 PGMTIVCGDSHT+THGAFGALA GIGTSEVEHVLATQTL Q +AK M + V G G+T Sbjct: 123 PGMTIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLIQSKAKNMLVRVDGVLPAGVT 182 Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239 AKDI+LAIIG+ G+AGGTG+V+E+ GEAIR LSMEGRMT+CNM+IE GA+AGL+APDETT Sbjct: 183 AKDIILAIIGEIGTAGGTGYVIEYAGEAIRALSMEGRMTICNMSIEGGARAGLIAPDETT 242 Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299 F YVK + APKG+ +D A+ YWKTLQ+DEGA FD VV L A ++ P V+WG++P VIS Sbjct: 243 FAYVKDKPRAPKGEAWDMALEYWKTLQSDEGAHFDKVVVLNAADLPPIVSWGSSPEDVIS 302 Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359 V +P+P D +R+S +AL YMGLKPG P+T++ +D+VFIGSCTN RIEDLR A Sbjct: 303 VTGAVPNPDEIPDETKRSSKWRALDYMGLKPGTPITDIKLDRVFIGSCTNGRIEDLREVA 362 Query: 360 EIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419 ++ +G VAP V A++VPGSG VK QAEAEGLDKIF AGF+WR PGCSMCLAMN+DRL Sbjct: 363 KVVEGHTVAPTVDAMIVPGSGLVKQQAEAEGLDKIFKAAGFDWREPGCSMCLAMNDDRLK 422 Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNIK 466 PGERCASTSNRNFEGRQG GRTHLVSPAMAAAAA+ GHF DIR K Sbjct: 423 PGERCASTSNRNFEGRQGFKGRTHLVSPAMAAAAAIAGHFVDIREWK 469 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: 790 Number of extensions: 30 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: 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_106714736.1 CU100_RS01185 (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.2425373.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-248 809.3 0.0 5.2e-248 809.1 0.0 1.0 1 NCBI__GCF_003010935.1:WP_106714736.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106714736.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 809.1 0.0 5.2e-248 5.2e-248 2 465 .. 4 467 .. 3 468 .. 0.99 Alignments for each domain: == domain 1 score: 809.1 bits; conditional E-value: 5.2e-248 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistes.rdve 73 ++tly+k++d h+v +e++t llyidrhlvhevtspqafeglr +grkvr+++ktla +dhni+t r NCBI__GCF_003010935.1:WP_106714736.1 4 PRTLYDKIWDDHLVDSQEDGTCLLYIDRHLVHEVTSPQAFEGLRLTGRKVRHPEKTLAVVDHNIPTSPdRTKR 76 8*****************************************************************8625667 PP TIGR00170 74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146 i ++++++qv++l +n+ +fgv+++ ++ +qgivh++gpe+g+tlpg+tivcgdsht+thgafgala gigt NCBI__GCF_003010935.1:WP_106714736.1 77 IENNESRIQVEALARNALDFGVEYYSEKDIRQGIVHIIGPEQGFTLPGMTIVCGDSHTSTHGAFGALAHGIGT 149 88899******************************************************************** PP TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219 sevehvlatqtl+q++ak++ ++v+g l g+takdiilaiig ig+aggtgyv+e+ageair+lsme+rmt+ NCBI__GCF_003010935.1:WP_106714736.1 150 SEVEHVLATQTLIQSKAKNMLVRVDGVLPAGVTAKDIILAIIGEIGTAGGTGYVIEYAGEAIRALSMEGRMTI 222 ************************************************************************* PP TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292 cnm+ie ga+agliapdettf+yvkd++ apkg+ ++ a++ywktl++dega+fdkvv+l+a d+ p v+wg NCBI__GCF_003010935.1:WP_106714736.1 223 CNMSIEGGARAGLIAPDETTFAYVKDKPRAPKGEAWDMALEYWKTLQSDEGAHFDKVVVLNAADLPPIVSWGS 295 ************************************************************************* PP TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365 +p++v+sv++ vp+p+++ d+ +++s +al+y+gl+pgt+++dik+d+vfigsctn+riedlr+ a+vv g+ NCBI__GCF_003010935.1:WP_106714736.1 296 SPEDVISVTGAVPNPDEIPDETKRSSKWRALDYMGLKPGTPITDIKLDRVFIGSCTNGRIEDLREVAKVVEGH 368 ************************************************************************* PP TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438 va++v a++vpgsglvk+qae+egldkif +agf+wre+gcs+cl+mn+d+l+++ercastsnrnfegrqg NCBI__GCF_003010935.1:WP_106714736.1 369 TVAPTVD-AMIVPGSGLVKQQAEAEGLDKIFKAAGFDWREPGCSMCLAMNDDRLKPGERCASTSNRNFEGRQG 440 *******.***************************************************************** PP TIGR00170 439 kgarthlvspamaaaaavagkfvdire 465 ++rthlvspamaaaaa+ag+fvdire NCBI__GCF_003010935.1:WP_106714736.1 441 FKGRTHLVSPAMAAAAAIAGHFVDIRE 467 **************************8 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 16.43 // [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