Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate BWI76_RS04670 BWI76_RS04670 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__Koxy:BWI76_RS04670 Length = 466 Score = 900 bits (2326), Expect = 0.0 Identities = 446/466 (95%), Positives = 458/466 (98%) Query: 1 MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60 MAKTLYEKLFDAHVVYEA+NETPLLYIDRHLVHEVTSPQAFDGLRAH RPVRQPGKTFAT Sbjct: 1 MAKTLYEKLFDAHVVYEAQNETPLLYIDRHLVHEVTSPQAFDGLRAHKRPVRQPGKTFAT 60 Query: 61 MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120 MDHNVSTQTKDINA GEMARIQMQELIKNCKEFGVELYDLNHP+QGIVHVMGPEQGVTLP Sbjct: 61 MDHNVSTQTKDINASGEMARIQMQELIKNCKEFGVELYDLNHPFQGIVHVMGPEQGVTLP 120 Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEV+GKAAPGITA Sbjct: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVKGKAAPGITA 180 Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPD+TTF Sbjct: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDQTTF 240 Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300 +YVKGRLHAPKG DF DAVAYWKTL TD+GATFD+VVTLQAEEI+PQVTWGTNPGQVISV Sbjct: 241 DYVKGRLHAPKGVDFADAVAYWKTLTTDDGATFDSVVTLQAEEIAPQVTWGTNPGQVISV 300 Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360 D IPDPASF+DPVERASAEKALAYMGLK G+PLTEVAIDKVFIGSCTNSRIEDLRAAAE Sbjct: 301 TDIIPDPASFSDPVERASAEKALAYMGLKSGVPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360 Query: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP Sbjct: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420 Query: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNIK 466 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR++K Sbjct: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRSLK 466 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: 973 Number of extensions: 21 Number of successful extensions: 1 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: 466 Length adjustment: 33 Effective length of query: 433 Effective length of database: 433 Effective search space: 187489 Effective search space used: 187489 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 BWI76_RS04670 BWI76_RS04670 (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.2973.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-280 914.1 0.8 8.2e-280 914.0 0.8 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS04670 BWI76_RS04670 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS04670 BWI76_RS04670 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 914.0 0.8 8.2e-280 8.2e-280 1 465 [. 1 464 [. 1 465 [. 1.00 Alignments for each domain: == domain 1 score: 914.0 bits; conditional E-value: 8.2e-280 TIGR00170 1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrd 71 maktlyeklfdahvv+ea+net+llyidrhlvhevtspqaf+glra+ r+vr+++kt+at+dhn+st+++d lcl|FitnessBrowser__Koxy:BWI76_RS04670 1 MAKTLYEKLFDAHVVYEAQNETPLLYIDRHLVHEVTSPQAFDGLRAHKRPVRQPGKTFATMDHNVSTQTKD 71 89********************************************************************* PP TIGR00170 72 veikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalaf 142 +++ +e+a++q++el kn+kefgv+l+dl++ qgivhv+gpe+g+tlpg+tivcgdshtathgafgalaf lcl|FitnessBrowser__Koxy:BWI76_RS04670 72 INASGEMARIQMQELIKNCKEFGVELYDLNHPFQGIVHVMGPEQGVTLPGMTIVCGDSHTATHGAFGALAF 142 *********************************************************************** PP TIGR00170 143 gigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsm 213 gigtsevehvlatqtlkq+rakt+kiev+gk+a+gitakdi+laiigk+g+aggtg+vvef+geairdlsm lcl|FitnessBrowser__Koxy:BWI76_RS04670 143 GIGTSEVEHVLATQTLKQGRAKTMKIEVKGKAAPGITAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSM 213 *********************************************************************** PP TIGR00170 214 eermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdi 284 e+rmt+cnmaie+gakagl+apd+ttf+yvk+r +apkg +f +avaywktl td+ga+fd vvtl+a++i lcl|FitnessBrowser__Koxy:BWI76_RS04670 214 EGRMTLCNMAIEMGAKAGLVAPDQTTFDYVKGRLHAPKGVDFADAVAYWKTLTTDDGATFDSVVTLQAEEI 284 *********************************************************************** PP TIGR00170 285 spqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedl 355 +pqvtwgtnpgqv+sv++ +pdp+s++dpve+asaekalay+gl++g++l+++++dkvfigsctnsriedl lcl|FitnessBrowser__Koxy:BWI76_RS04670 285 APQVTWGTNPGQVISVTDIIPDPASFSDPVERASAEKALAYMGLKSGVPLTEVAIDKVFIGSCTNSRIEDL 355 *********************************************************************** PP TIGR00170 356 raaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyerca 426 raaae++kg+kva++v+ alvvpgsg+vk+qae+egldkif+eagfewr +gcs+cl+mnnd+l+++erca lcl|FitnessBrowser__Koxy:BWI76_RS04670 356 RAAAEIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGERCA 425 *****************.***************************************************** PP TIGR00170 427 stsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465 stsnrnfegrqg+g+rthlvspamaaaaav+g+f+dir lcl|FitnessBrowser__Koxy:BWI76_RS04670 426 STSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRS 464 **************************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (466 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: 00:00:00.02 # Mc/sec: 7.27 // [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