Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate GFF2606 PGA1_c26470 2-isopropylmalate synthase LeuA
Query= BRENDA::Q9JZG1 (517 letters) >FitnessBrowser__Phaeo:GFF2606 Length = 523 Score = 484 bits (1246), Expect = e-141 Identities = 252/498 (50%), Positives = 341/498 (68%), Gaps = 4/498 (0%) Query: 5 NRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIA 64 +RV+IFDTTLRDGEQSPGA MT +EK+ +A L+ +GVDIIEAGF AS GDF+AV+ IA Sbjct: 8 DRVLIFDTTLRDGEQSPGATMTHDEKLEIAELLDDMGVDIIEAGFPIASEGDFKAVSEIA 67 Query: 65 KTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAA 124 + S +C L+RA +DI + EAV A + RIHTFI TSP+H + ++ E Sbjct: 68 ERSKNSRICGLARANFKDIDRCAEAVKRAAQPRIHTFIGTSPLHRAIP-NLTKDEMAEKI 126 Query: 125 VKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEE 184 V AR D+V++S DA R+E D+L + I+AGATTINIPDTVGY+ P ++ + Sbjct: 127 HDTVTHARNLVDNVQWSPMDATRTEWDYLCRVIEIAIKAGATTINIPDTVGYTAPVESAD 186 Query: 185 FFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASVE 244 + LI P V+++ HCHNDLG+A ANSLAA+ GGARQ+ECT+NGLGERAGN ++E Sbjct: 187 LIKRLIETVPGADDVIFATHCHNDLGMATANSLAAVAGGARQIECTINGLGERAGNTALE 246 Query: 245 EIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQD 304 E+VMALKVR+D+ TGIDT +I+ S+ VST++G+ VQPNKAIVG NAF+HESGIHQD Sbjct: 247 EVVMALKVRNDIMPFTTGIDTQKIMHISRRVSTVSGFVVQPNKAIVGKNAFAHESGIHQD 306 Query: 305 GVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARFK 364 G+LK++ET+EIM E VG A L LGK SGR A + KL+ LG E+ + L F RFK Sbjct: 307 GMLKNKETFEIMRPEDVGIAGTSLPLGKHSGRAALRDKLSQLGFEV-GDNQLKDLFVRFK 365 Query: 365 ELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEKRA 424 ELAD+K+E+FD+D+ AL+ + K +S K+ TG A + ++G++ Sbjct: 366 ELADRKKEVFDDDIIALM--RTSGDEDDHLKLVSMKVVCGTGGPAEATLEMEVEGKDVSE 423 Query: 425 SATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGAD 484 +A G GPVDA F+AI + + A LQ+Y V+AVT+GT++Q SVRL + G+ A+ Sbjct: 424 TAEGDGPVDAAFRAIRKIHPNSAHLQLYQVHAVTEGTDAQATVSVRLEENGVIATGESAN 483 Query: 485 TDVLVATAKAYLSALSKL 502 TD +VA+A AY+ AL++L Sbjct: 484 TDTVVASAAAYIGALNRL 501 Lambda K H 0.313 0.129 0.352 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: 636 Number of extensions: 21 Number of successful extensions: 4 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: 517 Length of database: 523 Length adjustment: 35 Effective length of query: 482 Effective length of database: 488 Effective search space: 235216 Effective search space used: 235216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 52 (24.6 bits)
Align candidate GFF2606 PGA1_c26470 (2-isopropylmalate synthase LeuA)
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))
# 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/TIGR00973.hmm # target sequence database: /tmp/gapView.15862.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00973 [M=494] Accession: TIGR00973 Description: leuA_bact: 2-isopropylmalate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-206 671.8 4.1 3e-206 671.6 4.1 1.0 1 lcl|FitnessBrowser__Phaeo:GFF2606 PGA1_c26470 2-isopropylmalate sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF2606 PGA1_c26470 2-isopropylmalate synthase LeuA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 671.6 4.1 3e-206 3e-206 1 494 [] 9 499 .. 9 499 .. 0.99 Alignments for each domain: == domain 1 score: 671.6 bits; conditional E-value: 3e-206 TIGR00973 1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravek 76 rvlifdttlrdGeq+pga++t +ekl+ia+ l+++gvdiieaGfp++s+gdf+av +ia++ kn+r++glara k lcl|FitnessBrowser__Phaeo:GFF2606 9 RVLIFDTTLRDGEQSPGATMTHDEKLEIAELLDDMGVDIIEAGFPIASEGDFKAVSEIAERSKNSRICGLARANFK 84 799************************************************************************* PP TIGR00973 77 didaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvv 152 did aea+k a++ rihtfi ts++h++ tkde+ e+i+ +v++a+n+vd+v++s+ da+rte ++l+rv+ lcl|FitnessBrowser__Phaeo:GFF2606 85 DIDRCAEAVKRAAQPRIHTFIGTSPLHRAIP-NLTKDEMAEKIHDTVTHARNLVDNVQWSPMDATRTEWDYLCRVI 159 ***************************9875.789***************************************** PP TIGR00973 153 eaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinG 228 e ai+aGattiniPdtvGy++P e ++lik+l e+vP+ d++i++ hch+dlG+a+anslaav Garq+ectinG lcl|FitnessBrowser__Phaeo:GFF2606 160 EIAIKAGATTINIPDTVGYTAPVESADLIKRLIETVPGADDVIFATHCHNDLGMATANSLAAVAGGARQIECTING 235 **************************************************************************** PP TIGR00973 229 iGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlkn 304 +GeraGn+aleevvmalkvr+d+++ +tgi+t++i+++sr vs ++g +vq+nkaivG+nafahesGihqdG+lkn lcl|FitnessBrowser__Phaeo:GFF2606 236 LGERAGNTALEEVVMALKVRNDIMPFTTGIDTQKIMHISRRVSTVSGFVVQPNKAIVGKNAFAHESGIHQDGMLKN 311 **************************************************************************** PP TIGR00973 305 ketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleel 380 ket+ei++pe++G+ + l lgk+sGraal+++l++lGf++ +++l+ lf +fkelad+kkevfd+d+ al+ ++ lcl|FitnessBrowser__Phaeo:GFF2606 312 KETFEIMRPEDVGIAGTSLPLGKHSGRAALRDKLSQLGFEVGDNQLKDLFVRFKELADRKKEVFDDDIIALMRTSG 387 **********************************************************************998765 PP TIGR00973 381 rqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkd 456 e+++lkl++++v +g+ + at++++v+g++ +++a G Gpvda ++ai ki + +l+ y+++a++eg+d lcl|FitnessBrowser__Phaeo:GFF2606 388 D--EDDHLKLVSMKVVCGTGGPAEATLEMEVEGKDVSETAEGDGPVDAAFRAIRKIHPNSAHLQLYQVHAVTEGTD 461 5..66778******************************************************************** PP TIGR00973 457 algevkvvlelngkkysGrgvatdiveasakayvnaln 494 a++ v+v+le ng+ ++G +++td v asa ay+ aln lcl|FitnessBrowser__Phaeo:GFF2606 462 AQATVSVRLEENGVIATGESANTDTVVASAAAYIGALN 499 ************************************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (494 nodes) Target sequences: 1 (523 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: 00:00:00.02 # Mc/sec: 9.36 // [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