Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate 7026626 Shewana3_3759 isopropylmalate isomerase large subunit (RefSeq)
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__ANA3:7026626 Length = 474 Score = 699 bits (1803), Expect = 0.0 Identities = 340/461 (73%), Positives = 394/461 (85%) Query: 3 KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62 KTLY+K++DAHVV E E P++Y+DRHLVHEVTSPQAF GL+ GR +R P KTFATMD Sbjct: 11 KTLYQKVWDAHVVATPEGEAPIIYVDRHLVHEVTSPQAFSGLKVAGRKLRAPEKTFATMD 70 Query: 63 HNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122 HN ST++ ++A MAR Q++ L +NCK+FGV LYD++HP QGIVHVMGPE G+TLPG Sbjct: 71 HNTSTRSASLDALSPMARTQVETLAQNCKDFGVRLYDIHHPNQGIVHVMGPELGITLPGT 130 Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182 IVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTL+Q +AKTMKIEV+G+ G+TAKD Sbjct: 131 VIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLRQLKAKTMKIEVRGQVTDGVTAKD 190 Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242 IVLAIIGK G GGTG+VVEFCGEAI LSMEGRMT+CNMAIEMGAKAG+VAPD+TTF+Y Sbjct: 191 IVLAIIGKIGMDGGTGYVVEFCGEAIEALSMEGRMTVCNMAIEMGAKAGMVAPDQTTFDY 250 Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302 ++GR APKG+D+ +AVA WK L+TD GA FD V L A I+PQ+TWGTNPGQV++++ Sbjct: 251 LEGREFAPKGEDWAEAVAAWKALKTDVGAEFDATVVLDAANIAPQLTWGTNPGQVVAIDA 310 Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362 +P+PA A+P RAS EKAL Y+GL G P+T+VAI+KVFIGSCTNSRIEDLR+AA+ A Sbjct: 311 PVPNPADEANPTIRASMEKALDYIGLTAGTPMTDVAINKVFIGSCTNSRIEDLRSAAKQA 370 Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422 KGRKVA GV A+VVPGSG VKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMN+DRL G+ Sbjct: 371 KGRKVASGVTAIVVPGSGQVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNDDRLEAGD 430 Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463 RCASTSNRNFEGRQGRG RTHLVSPAMAAAAA+ GHF DIR Sbjct: 431 RCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAIAGHFVDIR 471 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: 773 Number of extensions: 15 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: 474 Length adjustment: 33 Effective length of query: 433 Effective length of database: 441 Effective search space: 190953 Effective search space used: 190953 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 7026626 Shewana3_3759 (isopropylmalate isomerase large subunit (RefSeq))
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.27445.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-256 837.8 2.1 1.2e-256 837.6 2.1 1.0 1 lcl|FitnessBrowser__ANA3:7026626 Shewana3_3759 isopropylmalate is Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7026626 Shewana3_3759 isopropylmalate isomerase large subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 837.6 2.1 1.2e-256 1.2e-256 2 465 .. 10 472 .. 9 473 .. 1.00 Alignments for each domain: == domain 1 score: 837.6 bits; conditional E-value: 1.2e-256 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdveikeek 78 +ktly+k++dahvv e+e++++y+drhlvhevtspqaf gl++agrk+r ++kt+at+dhn st+s ++++ + lcl|FitnessBrowser__ANA3:7026626 10 PKTLYQKVWDAHVVATPEGEAPIIYVDRHLVHEVTSPQAFSGLKVAGRKLRAPEKTFATMDHNTSTRSASLDALSPM 86 8**************************************************************************** PP TIGR00170 79 aklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigtsevehvlat 155 a+ qv++l +n+k+fgv+l+d+++ +qgivhv+gpe g+tlpg+ ivcgdshtathgafgalafgigtsevehvlat lcl|FitnessBrowser__ANA3:7026626 87 ARTQVETLAQNCKDFGVRLYDIHHPNQGIVHVMGPELGITLPGTVIVCGDSHTATHGAFGALAFGIGTSEVEHVLAT 163 ***************************************************************************** PP TIGR00170 156 qtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagl 232 qtl+q +akt+kiev+g++++g+takdi+laiigkig+ ggtgyvvef+geai++lsme+rmtvcnmaie+gakag+ lcl|FitnessBrowser__ANA3:7026626 164 QTLRQLKAKTMKIEVRGQVTDGVTAKDIVLAIIGKIGMDGGTGYVVEFCGEAIEALSMEGRMTVCNMAIEMGAKAGM 240 ***************************************************************************** PP TIGR00170 233 iapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnpgqvlsvneevpdpks 309 +apd+ttf+y+ +r++apkg+++ +ava wk+lktd ga+fd +v+l+a +i+pq+twgtnpgqv++++ vp+p++ lcl|FitnessBrowser__ANA3:7026626 241 VAPDQTTFDYLEGREFAPKGEDWAEAVAAWKALKTDVGAEFDATVVLDAANIAPQLTWGTNPGQVVAIDAPVPNPAD 317 ***************************************************************************** PP TIGR00170 310 ladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkq 386 a+p +as+ekal+y+gl++gt+++d++++kvfigsctnsriedlr+aa+ +kg+kva++v a+vvpgsg+vk+q lcl|FitnessBrowser__ANA3:7026626 318 EANPTIRASMEKALDYIGLTAGTPMTDVAINKVFIGSCTNSRIEDLRSAAKQAKGRKVASGVT-AIVVPGSGQVKAQ 393 **************************************************************9.************* PP TIGR00170 387 aekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdi 463 ae+egldkif+eagfewr +gcs+cl+mn+d+l++++rcastsnrnfegrqg+g+rthlvspamaaaaa+ag+fvdi lcl|FitnessBrowser__ANA3:7026626 394 AEAEGLDKIFIEAGFEWRLPGCSMCLAMNDDRLEAGDRCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAIAGHFVDI 470 ***************************************************************************** PP TIGR00170 464 re 465 r+ lcl|FitnessBrowser__ANA3:7026626 471 RK 472 97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (474 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.03 // [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