Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_085640439.1 MGEO_RS16685 2-isopropylmalate synthase
Query= BRENDA::Q9JZG1 (517 letters) >NCBI__GCF_002115805.1:WP_085640439.1 Length = 520 Score = 487 bits (1253), Expect = e-142 Identities = 259/504 (51%), Positives = 347/504 (68%), Gaps = 6/504 (1%) Query: 1 MTQTN--RVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFE 58 MTQT+ RV+IFDTTLRDGEQSPGA MT +EK+ +A L+ +GVDIIEAGF AS GDF Sbjct: 1 MTQTDKDRVVIFDTTLRDGEQSPGATMTHDEKLEIAELLDDMGVDIIEAGFPIASEGDFR 60 Query: 59 AVNAIAKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPK 118 AV+ IA+ + +C L+RA DI + EAV A + RIHTFI TSP+H + Sbjct: 61 AVSEIAQRSKDAVICGLARAQLPDIDRCWEAVRHAKQPRIHTFIGTSPLHRAIP-NLTQD 119 Query: 119 QVIEAAVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSI 178 ++ E + V AR D+V++S DA R+E D+L + I++GATTINIPDTVGY+ Sbjct: 120 EMAERIEQTVTHARNLCDNVQWSPMDATRTEWDYLCRVVEIAIKSGATTINIPDTVGYTA 179 Query: 179 PYKTEEFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERA 238 P ++ + R LI P VV++ HCHNDLG+A AN+LAA+ GGARQ+ECT+NGLGERA Sbjct: 180 PVESADLIRRLIETVPGADDVVFATHCHNDLGMATANALAAVAGGARQIECTINGLGERA 239 Query: 239 GNASVEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHE 298 GN ++EE+VMALKVR D+ TGIDT +I+ S+ V+T++G+PVQ NKAIVG NAF+HE Sbjct: 240 GNTALEEVVMALKVRGDIMPYTTGIDTKKIMHISRRVATVSGFPVQFNKAIVGKNAFAHE 299 Query: 299 SGIHQDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNA 358 SGIHQDG+LK+ ET+EIM E VG A L LGK SGR A + KL +LG+E+ + L Sbjct: 300 SGIHQDGMLKNAETFEIMRPEDVGIAGTSLPLGKHSGRAALRAKLKELGVEV-GDNQLKD 358 Query: 359 AFARFKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIK 418 F RFK+LAD+K+E+FD+D+ ALV+ + ++ + ++ K+ TG A + I Sbjct: 359 IFVRFKDLADRKKEVFDDDILALVT--ATTEGDDALQLVNLKVVCGTGGPAEATLEMEIN 416 Query: 419 GEEKRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVV 478 GE+K A + G GPVDA FKAI + + A LQ+Y V+AVT+GT++Q SVRL + Sbjct: 417 GEDKSAVSEGDGPVDATFKAIRMLHPNKARLQLYQVHAVTEGTDAQATVSVRLEEDGMIA 476 Query: 479 NGQGADTDVLVATAKAYLSALSKL 502 GQ ADTD +VA+AKAY+ AL++L Sbjct: 477 TGQSADTDTVVASAKAYIHALNRL 500 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: 639 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: 520 Length adjustment: 35 Effective length of query: 482 Effective length of database: 485 Effective search space: 233770 Effective search space used: 233770 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 WP_085640439.1 MGEO_RS16685 (2-isopropylmalate synthase)
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.605078.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-202 658.9 2.1 2.3e-202 658.8 2.1 1.0 1 NCBI__GCF_002115805.1:WP_085640439.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085640439.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 658.8 2.1 2.3e-202 2.3e-202 1 494 [] 8 498 .. 8 498 .. 0.99 Alignments for each domain: == domain 1 score: 658.8 bits; conditional E-value: 2.3e-202 TIGR00973 1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglara 73 rv+ifdttlrdGeq+pga++t +ekl+ia+ l+++gvdiieaGfp++s+gdf av +ia++ k+a+++glara NCBI__GCF_002115805.1:WP_085640439.1 8 RVVIFDTTLRDGEQSPGATMTHDEKLEIAELLDDMGVDIIEAGFPIASEGDFRAVSEIAQRSKDAVICGLARA 80 799********************************************************************** PP TIGR00973 74 vekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrtele 146 did +ea++ a++ rihtfi ts++h++ t+de+ eri+++v++a+n+ d+v++s+ da+rte + NCBI__GCF_002115805.1:WP_085640439.1 81 QLPDIDRCWEAVRHAKQPRIHTFIGTSPLHRAIP-NLTQDEMAERIEQTVTHARNLCDNVQWSPMDATRTEWD 152 ******************************9875.789*********************************** PP TIGR00973 147 flarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGa 219 +l+rvve ai++GattiniPdtvGy++P e ++li++l e+vP+ d+++++ hch+dlG+a+an+laav Ga NCBI__GCF_002115805.1:WP_085640439.1 153 YLCRVVEIAIKSGATTINIPDTVGYTAPVESADLIRRLIETVPGADDVVFATHCHNDLGMATANALAAVAGGA 225 ************************************************************************* PP TIGR00973 220 rqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafah 292 rq+ectinG+GeraGn+aleevvmalkvr d+++++tgi+tk+i+++sr v+ ++g +vq nkaivG+nafah NCBI__GCF_002115805.1:WP_085640439.1 226 RQIECTINGLGERAGNTALEEVVMALKVRGDIMPYTTGIDTKKIMHISRRVATVSGFPVQFNKAIVGKNAFAH 298 ************************************************************************* PP TIGR00973 293 esGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkk 365 esGihqdG+lkn et+ei++pe++G+ + l lgk+sGraal+ +l+elG+++ +++l+ +f +fk+lad+kk NCBI__GCF_002115805.1:WP_085640439.1 299 ESGIHQDGMLKNAETFEIMRPEDVGIAGTSLPLGKHSGRAALRAKLKELGVEVGDNQLKDIFVRFKDLADRKK 371 ************************************************************************* PP TIGR00973 366 evfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekile 438 evfd+d+ alv+ ++ ++ l+l++l+v +g+ + at++++++ge+k+a++ G Gpvda++kai + NCBI__GCF_002115805.1:WP_085640439.1 372 EVFDDDILALVTATTE--GDDALQLVNLKVVCGTGGPAEATLEMEINGEDKSAVSEGDGPVDATFKAIRMLHP 442 ***********98776..45568************************************************** PP TIGR00973 439 levklleysitakgegkdalgevkvvlelngkkysGrgvatdiveasakayvnaln 494 + +l+ y+++a++eg+da++ v+v+le +g ++G++++td v asakay++aln NCBI__GCF_002115805.1:WP_085640439.1 443 NKARLQLYQVHAVTEGTDAQATVSVRLEEDGMIATGQSADTDTVVASAKAYIHALN 498 *******************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (494 nodes) Target sequences: 1 (520 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 23.71 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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