Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_018123429.1 B149_RS0101705 3-isopropylmalate dehydratase large subunit
Query= reanno::DvH:208495 (419 letters) >NCBI__GCF_000375485.1:WP_018123429.1 Length = 419 Score = 610 bits (1572), Expect = e-179 Identities = 301/419 (71%), Positives = 339/419 (80%) Query: 1 MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60 M+ TLA+KILQ+HTDE + GQIV+CRVS VLANDITAPLAIK+FR MGAK+VFD+DRV Sbjct: 1 MSQTLAEKILQQHTDETVEGPGQIVQCRVSGVLANDITAPLAIKAFREMGAKKVFDQDRV 60 Query: 61 ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120 LV DHFTP +DI++A+QVK+ REFA EMGVT+YYE GD GVEHALLPE GLVGPGD+V+ Sbjct: 61 FLVCDHFTPNRDIDSAEQVKVVREFAEEMGVTNYYECGDVGVEHALLPEKGLVGPGDIVI 120 Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180 GADSHTCTYGGLGAFATG+GSTD+ AMALGETWFKVPPTIR TG YVGAKD++L Sbjct: 121 GADSHTCTYGGLGAFATGMGSTDIGAAMALGETWFKVPPTIRVQVTGKASQYVGAKDVML 180 Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240 LIG IGV GALY+ALEF G I + VEGRMT+ANMAIEAGGK GLFAAD KT+ Y Sbjct: 181 NLIGRIGVAGALYKALEFGGETIADMTVEGRMTIANMAIEAGGKVGLFAADGKTIDYVVE 240 Query: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300 AGR + D A YER + DV GM P VACPHLPDNVKPV E + + Q VIGSC Sbjct: 241 AGRKNAEMLAPDPDAQYERVVDIDVNGMEPQVACPHLPDNVKPVDETAGLKIHQAVIGSC 300 Query: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360 TNGRI D+REAAA+L+ RKV + VRCIVLPATP IW+ L EGL+E FM+AGCIVGP TC Sbjct: 301 TNGRIEDMREAAAILKNRKVDKSVRCIVLPATPKIWQDCLSEGLMEIFMQAGCIVGPPTC 360 Query: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDPSTL 419 GPCLGGHMGILA GERAIATTNRNFKGRMGSLESEV+LS P+ AAASAV G I P+ L Sbjct: 361 GPCLGGHMGILAGGERAIATTNRNFKGRMGSLESEVFLSNPSVAAASAVAGEIIHPAKL 419 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: 641 Number of extensions: 22 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: 419 Length of database: 419 Length adjustment: 32 Effective length of query: 387 Effective length of database: 387 Effective search space: 149769 Effective search space used: 149769 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 WP_018123429.1 B149_RS0101705 (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.5708.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-194 632.2 1.6 2.3e-194 632.0 1.6 1.0 1 lcl|NCBI__GCF_000375485.1:WP_018123429.1 B149_RS0101705 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000375485.1:WP_018123429.1 B149_RS0101705 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 632.0 1.6 2.3e-194 2.3e-194 2 418 .. 4 418 .. 3 419 .] 0.99 Alignments for each domain: == domain 1 score: 632.0 bits; conditional E-value: 2.3e-194 TIGR02083 2 tlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnkd 70 tlaekil +++ pg+++ ++ vl+nd+t+plaikaf+e+g+kkvfd+d+v lv dhftpn+d lcl|NCBI__GCF_000375485.1:WP_018123429.1 4 TLAEKILQQHTDETVEGPGQIVQCRVSGVLANDITAPLAIKAFREMGAKKVFDQDRVFLVCDHFTPNRD 72 89*********999888**************************************************** PP TIGR02083 71 ikaaeqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvgs 139 i +aeqvk++refa e ++ +y+e g++gvehallpekglv +gd++igadshtctyg lgafatg+gs lcl|NCBI__GCF_000375485.1:WP_018123429.1 73 IDSAEQVKVVREFAEEMGVTNYYECGDVGVEHALLPEKGLVGPGDIVIGADSHTCTYGGLGAFATGMGS 141 ********************************************************************* PP TIGR02083 140 tdlavamatgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvdd 208 td+ +ama g++wfkvp +i++++ gk +yv akd++l++ig igv galyk+lef+ge++ +++v++ lcl|NCBI__GCF_000375485.1:WP_018123429.1 142 TDIGAAMALGETWFKVPPTIRVQVTGKASQYVGAKDVMLNLIGRIGVAGALYKALEFGGETIADMTVEG 210 ********************************************************************* PP TIGR02083 209 rltianmaieagaktgifevdektieyvkgrakrelkiykadedakyervieidlselepqvafphlpe 277 r+tianmaieag+k g+f +d kti+yv + ++++ ++ d da+yerv++id++ +epqva phlp+ lcl|NCBI__GCF_000375485.1:WP_018123429.1 211 RMTIANMAIEAGGKVGLFAADGKTIDYVVEAGRKNAEMLAPDPDAQYERVVDIDVNGMEPQVACPHLPD 279 ********************************************************************* PP TIGR02083 278 ntkeideaekeeikidqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkeglle 346 n k++de++ +ki q+vigsctngr+ed+r aa ilk++kv k+vr+i+lpa++k++ ++l egl+e lcl|NCBI__GCF_000375485.1:WP_018123429.1 280 NVKPVDETA--GLKIHQAVIGSCTNGRIEDMREAAAILKNRKVDKSVRCIVLPATPKIWQDCLSEGLME 346 *******99..9********************************************************* PP TIGR02083 347 ifieagavvstptcgpclgghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkias 415 if++ag++v++ptcgpclgghmgila gera++ttnrnf grmg +sev+l+ p vaaasa++g+i + lcl|NCBI__GCF_000375485.1:WP_018123429.1 347 IFMQAGCIVGPPTCGPCLGGHMGILAGGERAIATTNRNFKGRMGSLESEVFLSNPSVAAASAVAGEIIH 415 ********************************************************************9 PP TIGR02083 416 pee 418 p + lcl|NCBI__GCF_000375485.1:WP_018123429.1 416 PAK 418 987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (419 nodes) Target sequences: 1 (419 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: 00:00:00.01 # Mc/sec: 9.60 // [ok]
This GapMind analysis is from Apr 10 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