Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_013429581.1 CALKRO_RS02690 3-isopropylmalate dehydratase large subunit
Query= reanno::DvH:208495 (419 letters) >NCBI__GCF_000166775.1:WP_013429581.1 Length = 429 Score = 480 bits (1236), Expect = e-140 Identities = 232/417 (55%), Positives = 300/417 (71%), Gaps = 1/417 (0%) Query: 4 TLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRVALV 63 T++QKIL H + + G ++ V +VL ND+T P+AIK F +G RVFDKD++A+V Sbjct: 6 TMSQKILAYHAGKEYVEPGDLIFANVDLVLGNDVTTPVAIKEFEKIGIDRVFDKDKIAIV 65 Query: 64 MDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVVGAD 123 DHFTP KDI++AQQ K+ REFA++ +T+Y+E G+ G+EHALLPE GLV PGD+V+GAD Sbjct: 66 PDHFTPNKDIKSAQQCKMVREFAKKYEITNYFEVGEMGIEHALLPEKGLVVPGDLVIGAD 125 Query: 124 SHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLILTLI 183 SHTCTYG LGAF+TG+GSTD+A AMA G+ WFKVP I+ G + KD+IL +I Sbjct: 126 SHTCTYGALGAFSTGIGSTDMACAMATGKCWFKVPEAIKFILYGKKTGWTSGKDIILHII 185 Query: 184 GAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTTAGR 243 G IGVDGALY+++E+ G +++L ++ R T+ANMAIEAG K G+F D KT+ Y Sbjct: 186 GMIGVDGALYKSMEYTGEGLKSLSMDDRFTIANMAIEAGAKNGIFEVDEKTIEYVKQHST 245 Query: 244 TGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKD-VTVQQVVIGSCTN 302 F AD A Y + D++ + P VA PHLP+N K + E+ + + + QVVIGSCTN Sbjct: 246 KPYKIFKADEDAEYSQVFEIDISKIRPTVAFPHLPENTKTIDEITEKIYIDQVVIGSCTN 305 Query: 303 GRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATCGP 362 GRI DLR AA +L+GRKV + +RCI+ P T I++QAL+EGLIE F++AGC+V TCGP Sbjct: 306 GRIEDLRIAAKILKGRKVKKGLRCIIFPTTQNIYKQALKEGLIEIFIDAGCVVSTPTCGP 365 Query: 363 CLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419 CLGGHMGILADGE+A+ATTNRNF GRMG SEVYLS PA AAASAV G I P L Sbjct: 366 CLGGHMGILADGEKALATTNRNFVGRMGHPNSEVYLSSPAIAAASAVLGYIGSPEEL 422 Lambda K H 0.320 0.136 0.401 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: 519 Number of extensions: 20 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: 419 Length of database: 429 Length adjustment: 32 Effective length of query: 387 Effective length of database: 397 Effective search space: 153639 Effective search space used: 153639 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
Align candidate WP_013429581.1 CALKRO_RS02690 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR02083 (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/TIGR02083.hmm # target sequence database: /tmp/gapView.2414192.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02083 [M=419] Accession: TIGR02083 Description: LEU2: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-240 782.3 3.4 6.1e-240 782.2 3.4 1.0 1 NCBI__GCF_000166775.1:WP_013429581.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013429581.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 782.2 3.4 6.1e-240 6.1e-240 1 419 [] 5 422 .. 5 422 .. 1.00 Alignments for each domain: == domain 1 score: 782.2 bits; conditional E-value: 6.1e-240 TIGR02083 1 mtlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnkdika 73 mt+++kila +agke+v+pg+li a++dlvlgndvttp+aik+f ++g+++vfdkdk+a+v+dhftpnkdik+ NCBI__GCF_000166775.1:WP_013429581.1 5 MTMSQKILAYHAGKEYVEPGDLIFANVDLVLGNDVTTPVAIKEFEKIGIDRVFDKDKIAIVPDHFTPNKDIKS 77 9************************************************************************ PP TIGR02083 74 aeqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvgstdlavam 146 a+q+k++refak+ ei +yfe+ge+g+ehallpekglvv+gdl+igadshtctygalgaf+tg+gstd+a am NCBI__GCF_000166775.1:WP_013429581.1 78 AQQCKMVREFAKKYEITNYFEVGEMGIEHALLPEKGLVVPGDLVIGADSHTCTYGALGAFSTGIGSTDMACAM 150 ************************************************************************* PP TIGR02083 147 atgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvddrltianmaiea 219 atgk+wfkvpeaikf l gk + s+kd+il+iig+igvdgalyks+e++geglk+ls+ddr+tianmaiea NCBI__GCF_000166775.1:WP_013429581.1 151 ATGKCWFKVPEAIKFILYGKKTGWTSGKDIILHIIGMIGVDGALYKSMEYTGEGLKSLSMDDRFTIANMAIEA 223 ************************************************************************* PP TIGR02083 220 gaktgifevdektieyvkgrakrelkiykadedakyervieidlselepqvafphlpentkeideaekeeiki 292 gak+gifevdektieyvk+ +++ +ki+kadeda+y++v+eid+s+++p+vafphlpentk+ide++ e+i i NCBI__GCF_000166775.1:WP_013429581.1 224 GAKNGIFEVDEKTIEYVKQHSTKPYKIFKADEDAEYSQVFEIDISKIRPTVAFPHLPENTKTIDEIT-EKIYI 295 ******************************************************************9.9**** PP TIGR02083 293 dqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkeglleifieagavvstptcgpclg 365 dqvvigsctngr+edlr+aa+ilkg+kv+k +r+ii+p++q++y++alkegl+eifi+ag+vvstptcgpclg NCBI__GCF_000166775.1:WP_013429581.1 296 DQVVIGSCTNGRIEDLRIAAKILKGRKVKKGLRCIIFPTTQNIYKQALKEGLIEIFIDAGCVVSTPTCGPCLG 368 ************************************************************************* PP TIGR02083 366 ghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkiaspeev 419 ghmgila+ge+a++ttnrnfvgrmghp+sevyl+spa+aaasa+ g+i spee+ NCBI__GCF_000166775.1:WP_013429581.1 369 GHMGILADGEKALATTNRNFVGRMGHPNSEVYLSSPAIAAASAVLGYIGSPEEL 422 ***************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (419 nodes) Target sequences: 1 (429 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 26.30 // [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