Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate WP_014449007.1 LFE_RS04110 3-isopropylmalate dehydratase large subunit
Query= CharProtDB::CH_024771 (466 letters) >NCBI__GCF_000284315.1:WP_014449007.1 Length = 465 Score = 602 bits (1552), Expect = e-177 Identities = 296/464 (63%), Positives = 361/464 (77%), Gaps = 1/464 (0%) Query: 1 MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60 M +TL EK++D HVV E++ T LLYIDR LVHEVTSPQAF+GL+ GR V +P T A Sbjct: 1 MGRTLLEKIWDDHVVTESDGST-LLYIDRQLVHEVTSPQAFEGLKIAGRAVHRPQATLAV 59 Query: 61 MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120 DHNV T + ++ +Q++ L KN E+ V ++ ++ QG+VHV+ PEQG TLP Sbjct: 60 PDHNVPTTGRKKGIEDPISALQVETLTKNAMEYSVPIFTMDDIRQGVVHVIAPEQGFTLP 119 Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180 GMTIVCGDSHT+THGAFGALAFG+GTSEVEHV+ATQTL Q + K+ I+V G G T+ Sbjct: 120 GMTIVCGDSHTSTHGAFGALAFGVGTSEVEHVMATQTLIQKKPKSFLIKVNGHLPKGSTS 179 Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240 KD++L IIG+ G+ GGTG+V+EF GEA+R+LSME RMTLCNMAIE GA+AG++A DE TF Sbjct: 180 KDLILYIIGQIGTDGGTGYVLEFSGEAVRELSMEARMTLCNMAIEAGARAGMIAADEVTF 239 Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300 +Y+KGR APKG ++ AV+ WK+L +D A +D V+ + A I PQ+TWGTNPG V+ V Sbjct: 240 SYIKGRPMAPKGDLWEKAVSSWKSLHSDPDAKYDRVLEIDATRIEPQITWGTNPGMVLPV 299 Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360 +IP P SF D V + +A+ AL YMGL+PG PL+E++ID+VFIGSCTN RIEDLRAAA Sbjct: 300 TGSIPSPESFKDEVSKENAKNALKYMGLEPGTPLSEISIDRVFIGSCTNGRIEDLRAAAS 359 Query: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420 I KGRKV+P V A+VVPGSG V QAE EGLDKIF+EAGFEWR PGCSMCL MN D+L P Sbjct: 360 IIKGRKVSPSVNAMVVPGSGLVGQQAEKEGLDKIFLEAGFEWREPGCSMCLGMNPDQLLP 419 Query: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRN 464 GERCASTSNRNFEGRQGRGGRTHLVSP MAAAAA+TGHF DIRN Sbjct: 420 GERCASTSNRNFEGRQGRGGRTHLVSPEMAAAAAITGHFVDIRN 463 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: 751 Number of extensions: 25 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: 465 Length adjustment: 33 Effective length of query: 433 Effective length of database: 432 Effective search space: 187056 Effective search space used: 187056 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_014449007.1 LFE_RS04110 (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.3574365.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-241 787.9 0.0 1.5e-241 787.8 0.0 1.0 1 NCBI__GCF_000284315.1:WP_014449007.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000284315.1:WP_014449007.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 787.8 0.0 1.5e-241 1.5e-241 1 465 [. 1 463 [. 1 464 [. 0.99 Alignments for each domain: == domain 1 score: 787.8 bits; conditional E-value: 1.5e-241 TIGR00170 1 maktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesrdve 73 m +tl+ek++d hvv e+++ ++llyidr lvhevtspqafegl+ agr v r++ tla dhn++t+ r NCBI__GCF_000284315.1:WP_014449007.1 1 MGRTLLEKIWDDHVVTESDG-STLLYIDRQLVHEVTSPQAFEGLKIAGRAVHRPQATLAVPDHNVPTTGRKKG 72 789*************9987.579************************************************* PP TIGR00170 74 ikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafgalafgigt 146 i + + lqv++l+kn+ e+ v++f +++ +qg+vhv+ pe+g+tlpg+tivcgdsht+thgafgalafg+gt NCBI__GCF_000284315.1:WP_014449007.1 73 IEDPISALQVETLTKNAMEYSVPIFTMDDIRQGVVHVIAPEQGFTLPGMTIVCGDSHTSTHGAFGALAFGVGT 145 ************************************************************************* PP TIGR00170 147 sevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageairdlsmeermtv 219 sevehv+atqtl+q+++k++ i+v+g+l kg t+kd+il+iig+ig+ ggtgyv+ef+gea+r+lsme+rmt+ NCBI__GCF_000284315.1:WP_014449007.1 146 SEVEHVMATQTLIQKKPKSFLIKVNGHLPKGSTSKDLILYIIGQIGTDGGTGYVLEFSGEAVRELSMEARMTL 218 ************************************************************************* PP TIGR00170 220 cnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgt 292 cnmaieaga+ag+ia de+tf+y+k+r++apkg+ +ekav+ wk+l++d++ak+d+v+ ++a+ i pq+twgt NCBI__GCF_000284315.1:WP_014449007.1 219 CNMAIEAGARAGMIAADEVTFSYIKGRPMAPKGDLWEKAVSSWKSLHSDPDAKYDRVLEIDATRIEPQITWGT 291 ************************************************************************* PP TIGR00170 293 npgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsriedlraaaevvkgk 365 npg+vl+v++++p+p+s+ d+v+k++a++al+y+glepgt+l +i +d+vfigsctn+riedlraaa+++kg+ NCBI__GCF_000284315.1:WP_014449007.1 292 NPGMVLPVTGSIPSPESFKDEVSKENAKNALKYMGLEPGTPLSEISIDRVFIGSCTNGRIEDLRAAASIIKGR 364 ************************************************************************* PP TIGR00170 366 kvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmnndvldeyercastsnrnfegrqg 438 kv+++v+ a+vvpgsglv +qaekegldkifleagfewre+gcs+clgmn+d+l ++ercastsnrnfegrqg NCBI__GCF_000284315.1:WP_014449007.1 365 KVSPSVN-AMVVPGSGLVGQQAEKEGLDKIFLEAGFEWREPGCSMCLGMNPDQLLPGERCASTSNRNFEGRQG 436 *******.***************************************************************** PP TIGR00170 439 kgarthlvspamaaaaavagkfvdire 465 +g+rthlvsp maaaaa++g+fvdir+ NCBI__GCF_000284315.1:WP_014449007.1 437 RGGRTHLVSPEMAAAAAITGHFVDIRN 463 **************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (465 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: 00:00:00.00 # Mc/sec: 21.85 // [ok]
This GapMind analysis is from Jul 25 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