Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate WP_012673803.1 SULAZ_RS03795 3-isopropylmalate dehydratase large subunit
Query= reanno::DvH:208495 (419 letters) >NCBI__GCF_000021545.1:WP_012673803.1 Length = 431 Score = 480 bits (1235), Expect = e-140 Identities = 232/416 (55%), Positives = 304/416 (73%) Query: 1 MAHTLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSFRAMGAKRVFDKDRV 60 M T+ +KI+ H + + G++V +V + +ANDITAPLAIK G +V D +++ Sbjct: 1 MGMTITEKIIAAHAGKDYVEPGELVTVKVDLAIANDITAPLAIKQLEKYGIDKVHDPNKI 60 Query: 61 ALVMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120 ALVMDHF P KDI +AQQ+K++R+FA++MG+ +Y+EG D GV H LLPE G V PGD+V+ Sbjct: 61 ALVMDHFFPPKDILSAQQIKISRDFAKKMGIKNYFEGQDSGVMHTLLPEKGFVVPGDLVI 120 Query: 121 GADSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLIL 180 GADSHTCTYGG+GAF+TG+GSTD+A A GETW +VP T++ TF G +VG KD +L Sbjct: 121 GADSHTCTYGGIGAFSTGVGSTDIAYIWATGETWLRVPETMKFTFYGKPQKWVGGKDFVL 180 Query: 181 TLIGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTT 240 T+IG IGVDGALY+A+E+ G AI+ALD++ R+T+ANMAIEAGGK + AD KT+ + Sbjct: 181 TVIGKIGVDGALYKAMEYHGEAIKALDIDNRLTIANMAIEAGGKNAVIEADEKTIEWVRK 240 Query: 241 AGRTGDTAFSADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQVVIGSC 300 + +D A Y E FD + PVVACP+LP NVKPVSEV + QV IGSC Sbjct: 241 RTNREFKIYKSDPDAKYCCEYEFDANKIEPVVACPNLPSNVKPVSEVAGTHIDQVFIGSC 300 Query: 301 TNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIVGPATC 360 TNGR+ DLR AAA+L+G+KV +VRCIV+PA+ I++QAL EG+IE +AGC++ +TC Sbjct: 301 TNGRLSDLRIAAAILKGKKVHPEVRCIVIPASDQIYKQALHEGIIEILADAGCLISTSTC 360 Query: 361 GPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITDP 416 GPCLGGHMGILA+GE ++T+NRNF GRMG +S+VYLS PA AAASAV G I P Sbjct: 361 GPCLGGHMGILAEGEVCLSTSNRNFVGRMGHPKSQVYLSSPAVAAASAVLGRIAHP 416 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: 533 Number of extensions: 17 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: 431 Length adjustment: 32 Effective length of query: 387 Effective length of database: 399 Effective search space: 154413 Effective search space used: 154413 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_012673803.1 SULAZ_RS03795 (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.27631.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-205 669.2 1.4 1.3e-205 669.1 1.4 1.0 1 lcl|NCBI__GCF_000021545.1:WP_012673803.1 SULAZ_RS03795 3-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021545.1:WP_012673803.1 SULAZ_RS03795 3-isopropylmalate dehydratase large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 669.1 1.4 1.3e-205 1.3e-205 1 419 [] 3 419 .. 3 419 .. 1.00 Alignments for each domain: == domain 1 score: 669.1 bits; conditional E-value: 1.3e-205 TIGR02083 1 mtlaekiladkagkeevkpgelilakldlvlgndvttplaikafkelgvkkvfdkdkvalvldhftpnk 69 mt++eki+a +agk++v+pgel+++k+dl+++nd+t+plaik++ ++g++kv+d++k+alv+dhf p k lcl|NCBI__GCF_000021545.1:WP_012673803.1 3 MTITEKIIAAHAGKDYVEPGELVTVKVDLAIANDITAPLAIKQLEKYGIDKVHDPNKIALVMDHFFPPK 71 9******************************************************************** PP TIGR02083 70 dikaaeqvklirefakekeiekyfeigelgvehallpekglvvsgdliigadshtctygalgafatgvg 138 di +a+q+k++r+fak+ +i++yfe + gv h+llpekg+vv+gdl+igadshtctyg +gaf+tgvg lcl|NCBI__GCF_000021545.1:WP_012673803.1 72 DILSAQQIKISRDFAKKMGIKNYFEGQDSGVMHTLLPEKGFVVPGDLVIGADSHTCTYGGIGAFSTGVG 140 ********************************************************************* PP TIGR02083 139 stdlavamatgkawfkvpeaikfvlkgklkdyvsakdlilkiigkigvdgalykslefsgeglkelsvd 207 std+a atg++w++vpe++kf++ gk +++v +kd +l +igkigvdgalyk++e+ ge++k l +d lcl|NCBI__GCF_000021545.1:WP_012673803.1 141 STDIAYIWATGETWLRVPETMKFTFYGKPQKWVGGKDFVLTVIGKIGVDGALYKAMEYHGEAIKALDID 209 ********************************************************************* PP TIGR02083 208 drltianmaieagaktgifevdektieyvkgrakrelkiykadedakyervieidlselepqvafphlp 276 +rltianmaieag+k+ ++e+dektie+v++r++re+kiyk+d daky + e+d +++ep va p lp lcl|NCBI__GCF_000021545.1:WP_012673803.1 210 NRLTIANMAIEAGGKNAVIEADEKTIEWVRKRTNREFKIYKSDPDAKYCCEYEFDANKIEPVVACPNLP 278 ********************************************************************* PP TIGR02083 277 entkeideaekeeikidqvvigsctngrledlrlaaeilkgkkvakevrliilpasqkvylealkegll 345 +n k+++e++ +idqv igsctngrl+dlr+aa ilkgkkv +evr+i++pas+++y++al+eg++ lcl|NCBI__GCF_000021545.1:WP_012673803.1 279 SNVKPVSEVA--GTHIDQVFIGSCTNGRLSDLRIAAAILKGKKVHPEVRCIVIPASDQIYKQALHEGII 345 *********9..899****************************************************** PP TIGR02083 346 eifieagavvstptcgpclgghmgilaegeravsttnrnfvgrmghpksevylaspavaaasaikgkia 414 ei+ +ag+++st tcgpclgghmgilaege+++st+nrnfvgrmghpks+vyl+spavaaasa+ g+ia lcl|NCBI__GCF_000021545.1:WP_012673803.1 346 EILADAGCLISTSTCGPCLGGHMGILAEGEVCLSTSNRNFVGRMGHPKSQVYLSSPAVAAASAVLGRIA 414 ********************************************************************* PP TIGR02083 415 speev 419 +p+ev lcl|NCBI__GCF_000021545.1:WP_012673803.1 415 HPDEV 419 **997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (419 nodes) Target sequences: 1 (431 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: 7.73 // [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