Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_011734568.1 PPRO_RS09555 3-isopropylmalate dehydratase large subunit
Query= reanno::DvH:208495 (419 letters) >NCBI__GCF_000015045.1:WP_011734568.1 Length = 427 Score = 347 bits (890), Expect = e-100 Identities = 192/427 (44%), Positives = 261/427 (61%), Gaps = 15/427 (3%) Query: 1 MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60 M T+A+KI + H + +++R + +VL ++IT P+AI RVFD ++ Sbjct: 1 MPKTIAEKIFESHLVDEPFPGTKVLR--LDVVLCHEITTPIAIDDLVRRNKDRVFDSTKI 58 Query: 61 ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120 V+DH TP KD + A Q K+ R++AR + +++ G GV HAL PE G + PG V+ Sbjct: 59 KAVIDHVTPSKDSKTATQAKILRDWARRHDIPDFFDIGANGVCHALFPEKGFIRPGYTVI 118 Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180 DSHTCT+G GAFA G+G+TD+ + G F+ P TIR G LP V AKD+IL Sbjct: 119 MGDSHTCTHGAFGAFAAGIGTTDLEVGILKGVCAFRQPKTIRFNVIGQLPTGVYAKDVIL 178 Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTY--- 237 +IG IGV+GA R +EF G I A+ ++ RM + NMAIEAGG +G+ D T+ Y Sbjct: 179 HIIGRIGVNGATDRVMEFHGDTIAAMTMDSRMALCNMAIEAGGTSGICMPDMTTVDYLWP 238 Query: 238 -------CTTAGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDV 290 A + +D A YE+ + DVT + P V + PD VKPV+E+ Sbjct: 239 FISDEFESKEAALAEYGKWCSDPDASYEQVIDIDVTNLEPTVTFGYKPDQVKPVTELAGT 298 Query: 291 TVQQVVIGSCTNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFME 350 V Q+ +GSCTNGR+ DLR AA +L+G+K++ VR I+ PATP ++++AL+EGL+E FME Sbjct: 299 KVDQIYLGSCTNGRLEDLRIAAGILKGKKLAPHVRGILSPATPKVYQEALKEGLMEIFME 358 Query: 351 AG-CIVGPATCGPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAV 409 AG CI P TCG CLG G+LA+GE ATTNRNF GRMG V+L PATAAASA+ Sbjct: 359 AGFCITNP-TCGACLGMSNGVLAEGEVCAATTNRNFMGRMGK-GGMVHLMSPATAAASAI 416 Query: 410 TGVITDP 416 GVI DP Sbjct: 417 EGVIADP 423 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: 487 Number of extensions: 20 Number of successful extensions: 3 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: 427 Length adjustment: 32 Effective length of query: 387 Effective length of database: 395 Effective search space: 152865 Effective search space used: 152865 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_011734568.1 PPRO_RS09555 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR02086 (3-isopropylmalate dehydratase, large subunit)
# 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/TIGR02086.hmm # target sequence database: /tmp/gapView.31359.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02086 [M=411] Accession: TIGR02086 Description: IPMI_arch: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-135 437.1 0.2 3.3e-135 436.9 0.2 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011734568.1 PPRO_RS09555 3-isopropylmalate d Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011734568.1 PPRO_RS09555 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 436.9 0.2 3.3e-135 3.3e-135 1 410 [. 3 424 .. 3 425 .. 0.96 Alignments for each domain: == domain 1 score: 436.9 bits; conditional E-value: 3.3e-135 TIGR02086 1 ktlaekilsekvGkevkaGeivevkvDlvmvhDgtgplvikalrelg.akvekkekivlvfDhvvPapt 68 kt+aeki+ ++ e +G v+ + D+v+ h+ t+p +i l + ++v++ +ki v+Dhv+P+++ lcl|NCBI__GCF_000015045.1:WP_011734568.1 3 KTIAEKIFESHLVDEPFPGTKVL-RLDVVLCHEITTPIAIDDLVRRNkDRVFDSTKIKAVIDHVTPSKD 70 699****************9986.89**************999776669******************** PP TIGR02086 69 veaaelqkeirefakelgikv.fdvg.eGichqvlvekgyakpgkvvvgaDshtttsGalgafatGlGa 135 ++a k +r++a+++ i+ fd+g +G+ch ++ ekg+++pg+ v+ +Dsht+t+Ga+gafa G+G+ lcl|NCBI__GCF_000015045.1:WP_011734568.1 71 SKTATQAKILRDWARRHDIPDfFDIGaNGVCHALFPEKGFIRPGYTVIMGDSHTCTHGAFGAFAAGIGT 139 *********************9998637***************************************** PP TIGR02086 136 tDvalalatGktWlkvPesikveleGkleekvtakDvileivkelgadgatykaieftgeeiealslde 204 tD+ + ++ G ++ P++i+ ++ G+l v+akDvil+i++++g +gat +++ef+g++i a+++d+ lcl|NCBI__GCF_000015045.1:WP_011734568.1 140 TDLEVGILKGVCAFRQPKTIRFNVIGQLPTGVYAKDVILHIIGRIGVNGATDRVMEFHGDTIAAMTMDS 208 ********************************************************************* PP TIGR02086 205 Rltlsnlaveagakaglvepdeetleylkkrrge...........frilkadedakyeeeieidlsele 262 R++l+n+a+eag+ +g+ pd +t++yl ++ + +d+da+ye+ i+id+++le lcl|NCBI__GCF_000015045.1:WP_011734568.1 209 RMALCNMAIEAGGTSGICMPDMTTVDYLWPFISDefeskeaalaeYGKWCSDPDASYEQVIDIDVTNLE 277 ***************************976555555667777776667889****************** PP TIGR02086 263 plvavPhsvdnvkeveevegteidqvfiGsCtnGRledlkiaaeilegrevhkdvrlivvPasrkvyek 331 p+v+ +++d+vk+v+e gt++dq+++GsCtnGRledl+iaa il+g++ +++vr i +Pa kvy++ lcl|NCBI__GCF_000015045.1:WP_011734568.1 278 PTVTFGYKPDQVKPVTELAGTKVDQIYLGSCTNGRLEDLRIAAGILKGKKLAPHVRGILSPATPKVYQE 346 ********************************************************************* PP TIGR02086 332 aleeGlietlveaGaiiltpgCGPClGahlGvladgevivsttnRnfkGRmGspkaeiYLasPavaavs 400 al+eGl+e+++eaG i++p+CG ClG Gvla+gev+ +ttnRnf GRmG+ ++L sPa+aa+s lcl|NCBI__GCF_000015045.1:WP_011734568.1 347 ALKEGLMEIFMEAGFCITNPTCGACLGMSNGVLAEGEVCAATTNRNFMGRMGKG-GMVHLMSPATAAAS 414 ****************************************************75.78************ PP TIGR02086 401 aveGeitdpe 410 a+eG+i+dp+ lcl|NCBI__GCF_000015045.1:WP_011734568.1 415 AIEGVIADPR 424 ********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (411 nodes) Target sequences: 1 (427 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: 00:00:00.01 # Mc/sec: 10.06 // [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