Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate 8501056 DvMF_1792 3-isopropylmalate dehydratase large subunit (RefSeq)
Query= reanno::DvH:208495 (419 letters) >FitnessBrowser__Miya:8501056 Length = 418 Score = 724 bits (1870), Expect = 0.0 Identities = 359/419 (85%), Positives = 385/419 (91%), Gaps = 1/419 (0%) Query: 1 MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60 MAHTLAQKILQ HTDEAIT AGQIVRCRVS+ LANDITAPLAIKSFRAMGAK+VFD+D+V Sbjct: 1 MAHTLAQKILQAHTDEAITAAGQIVRCRVSLALANDITAPLAIKSFRAMGAKKVFDRDKV 60 Query: 61 ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120 ALVMDHFTPQKDI +AQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV Sbjct: 61 ALVMDHFTPQKDIASAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120 Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180 GADSHTCTYGGLGAFATG GSTDVAGAMALGETWFKVPPTIRATFTGTLP +VGAKDLIL Sbjct: 121 GADSHTCTYGGLGAFATGFGSTDVAGAMALGETWFKVPPTIRATFTGTLPKWVGAKDLIL 180 Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240 LIG IGVDGALYRALEFDGAAIEAL VEGRMT+ANMAIEAGGKAGLFAADAKTL Y Sbjct: 181 RLIGEIGVDGALYRALEFDGAAIEALSVEGRMTIANMAIEAGGKAGLFAADAKTLAYTAA 240 Query: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300 GR D SAD GA YEREL+FDV+GM P+VACPHLP+NVKPV EV+ VT+ QVVIGSC Sbjct: 241 RGRK-DAPLSADPGATYERELTFDVSGMEPLVACPHLPENVKPVGEVRGVTLDQVVIGSC 299 Query: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360 TNGRI D+REAA VL+GRKV++ VRCIVLPATPG+W++AL+EGLIETFME+GCIVGPATC Sbjct: 300 TNGRISDMREAAEVLKGRKVAKGVRCIVLPATPGVWKEALKEGLIETFMESGCIVGPATC 359 Query: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419 GPCLGGHMGILADGERAIATTNRNF+GRMGSLESEVYL+ PA AAASAV G+I P +L Sbjct: 360 GPCLGGHMGILADGERAIATTNRNFRGRMGSLESEVYLASPAVAAASAVAGIIAHPGSL 418 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: 718 Number of extensions: 23 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: 418 Length adjustment: 32 Effective length of query: 387 Effective length of database: 386 Effective search space: 149382 Effective search space used: 149382 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: 50 (23.9 bits)
Align candidate 8501056 DvMF_1792 (3-isopropylmalate dehydratase large subunit (RefSeq))
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.32503.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.8e-193 626.7 0.1 1.1e-192 626.4 0.1 1.0 1 lcl|FitnessBrowser__Miya:8501056 DvMF_1792 3-isopropylmalate dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501056 DvMF_1792 3-isopropylmalate dehydratase large subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 626.4 0.1 1.1e-192 1.1e-192 2 417 .. 4 416 .. 3 418 .] 0.99 Alignments for each domain: == domain 1 score: 626.4 bits; conditional E-value: 1.1e-192 TIGR02083 2 tlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnkdikaaeqvk 78 tla+kil ++ +g+++ ++ l+l+nd+t+plaik+f+ +g+kkvfd+dkvalv+dhftp+kdi +a+qvk lcl|FitnessBrowser__Miya:8501056 4 TLAQKILQAHTDEAITAAGQIVRCRVSLALANDITAPLAIKSFRAMGAKKVFDRDKVALVMDHFTPQKDIASAQQVK 80 89*************************************************************************** PP TIGR02083 79 lirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvgstdlavamatgkawfkv 155 l+refa+e ++ +y+e g+ gvehallpe glv +gd+++gadshtctyg lgafatg gstd+a+ama g++wfkv lcl|FitnessBrowser__Miya:8501056 81 LTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVVGADSHTCTYGGLGAFATGFGSTDVAGAMALGETWFKV 157 ***************************************************************************** PP TIGR02083 156 peaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvddrltianmaieagaktgifevdekt 232 p +i+ ++ g l ++v akdlil++ig+igvdgaly++lef g +++ lsv++r+tianmaieag+k+g+f +d kt lcl|FitnessBrowser__Miya:8501056 158 PPTIRATFTGTLPKWVGAKDLILRLIGEIGVDGALYRALEFDGAAIEALSVEGRMTIANMAIEAGGKAGLFAADAKT 234 ***************************************************************************** PP TIGR02083 233 ieyvkgrakrelkiykadedakyervieidlselepqvafphlpentkeideaekeeikidqvvigsctngrledlr 309 ++y+ r++++ + +ad a yer++ +d+s +ep va phlpen k++ e+ + +dqvvigsctngr++d+r lcl|FitnessBrowser__Miya:8501056 235 LAYTAARGRKDAPL-SADPGATYERELTFDVSGMEPLVACPHLPENVKPVGEVR--GVTLDQVVIGSCTNGRISDMR 308 ********999875.67************************************9..9******************** PP TIGR02083 310 laaeilkgkkvakevrliilpasqkvylealkeglleifieagavvstptcgpclgghmgilaegeravsttnrnfv 386 aae+lkg+kvak vr+i+lpa++ v++ealkegl+e+f+e+g++v++ tcgpclgghmgila+gera++ttnrnf lcl|FitnessBrowser__Miya:8501056 309 EAAEVLKGRKVAKGVRCIVLPATPGVWKEALKEGLIETFMESGCIVGPATCGPCLGGHMGILADGERAIATTNRNFR 385 ***************************************************************************** PP TIGR02083 387 grmghpksevylaspavaaasaikgkiaspe 417 grmg +sevylaspavaaasa++g+ia+p lcl|FitnessBrowser__Miya:8501056 386 GRMGSLESEVYLASPAVAAASAVAGIIAHPG 416 ****************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (419 nodes) Target sequences: 1 (418 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: 00:00:00.02 # Mc/sec: 7.58 // [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