Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate RR42_RS05465 RR42_RS05465 2-isopropylmalate synthase
Query= BRENDA::Q9JZG1 (517 letters) >lcl|FitnessBrowser__Cup4G11:RR42_RS05465 RR42_RS05465 2-isopropylmalate synthase Length = 512 Score = 639 bits (1647), Expect = 0.0 Identities = 318/506 (62%), Positives = 400/506 (79%), Gaps = 2/506 (0%) Query: 4 TNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAI 63 ++++IIFDTTLRDGEQSPGA+MT+EEKIR+ARQLE+L VD+IEAGFAA+S GDFEA+ +I Sbjct: 2 SDKLIIFDTTLRDGEQSPGASMTREEKIRIARQLERLKVDVIEAGFAASSNGDFEAIRSI 61 Query: 64 AKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEA 123 A+ + ST+CSL+RA +RDI +A EA+ PA RIHTFIATS +HME KL+M P QV E Sbjct: 62 AQVVKDSTICSLARANDRDIARAAEALKPANSFRIHTFIATSALHMEKKLRMTPDQVFEQ 121 Query: 124 AVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTE 183 A++AV+ AR++TDD+EFS ED RS++DFL + VI+ GATTIN+PDTVGY++P Sbjct: 122 AIQAVRFARQFTDDIEFSPEDGSRSDMDFLCRVLEGVIKEGATTINLPDTVGYAVPEGYA 181 Query: 184 EFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALK-GGARQVECTVNGLGERAGNAS 242 R + + PN K +WS HCHNDLG+AVANSLAA+K GGARQVECT+NGLGERAGN S Sbjct: 182 GLIRSVRERIPNSDKAIWSVHCHNDLGMAVANSLAAVKLGGARQVECTINGLGERAGNTS 241 Query: 243 VEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIH 302 +EE+VMA+K R D F ++ G+DTTQIVP+SKLVS ITG+ VQPNKA+VGANAF+H SGIH Sbjct: 242 LEEVVMAVKTRRDYFDMDVGVDTTQIVPASKLVSQITGFVVQPNKAVVGANAFAHASGIH 301 Query: 303 QDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFAR 362 QDGVLK R+TYEIM AE VGW+ N++ LGKLSGRNAFK +L +LGIELESE +NAAF R Sbjct: 302 QDGVLKARDTYEIMRAEDVGWSANKIVLGKLSGRNAFKQRLQELGIELESEGEVNAAFTR 361 Query: 363 FKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEK 422 FKELAD+K EIFDED+ A+VSDE +N E ++FIS +ETGE P A +VF++ G E Sbjct: 362 FKELADQKSEIFDEDIMAIVSDEAHDVN-EHFRFISLSQHSETGERPHARVVFNMDGNEV 420 Query: 423 RASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQG 482 G+GPVDA AIE SGA L +YSVNA+T GT++QGE +VRL++G R+VNG G Sbjct: 421 TGEGEGNGPVDATLHAIEGKVASGAELVLYSVNAITAGTQAQGEVTVRLSKGGRIVNGVG 480 Query: 483 ADTDVLVATAKAYLSALSKLEFSAAK 508 D D++ A+AKAYL+AL+KL A + Sbjct: 481 TDPDIVAASAKAYLAALNKLHDKAVQ 506 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: 695 Number of extensions: 18 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: 517 Length of database: 512 Length adjustment: 35 Effective length of query: 482 Effective length of database: 477 Effective search space: 229914 Effective search space used: 229914 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 RR42_RS05465 RR42_RS05465 (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.27177.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-216 705.1 5.2 2.3e-216 704.9 5.2 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS05465 RR42_RS05465 2-isopropylmalate s Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS05465 RR42_RS05465 2-isopropylmalate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 704.9 5.2 2.3e-216 2.3e-216 1 494 [] 4 498 .. 4 498 .. 0.99 Alignments for each domain: == domain 1 score: 704.9 bits; conditional E-value: 2.3e-216 TIGR00973 1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvg 69 +++ifdttlrdGeq+pgas+t eek++ia++lerl vd+ieaGf++ss+gdfea++ ia+ vk++++++ lcl|FitnessBrowser__Cup4G11:RR42_RS05465 4 KLIIFDTTLRDGEQSPGASMTREEKIRIARQLERLKVDVIEAGFAASSNGDFEAIRSIAQVVKDSTICS 72 689****************************************************************** PP TIGR00973 70 laravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsae 138 lara ++di aaealkpa+ +rihtfiats++h+e+kl++t d+v e++++av++a++f+dd+efs+e lcl|FitnessBrowser__Cup4G11:RR42_RS05465 73 LARANDRDIARAAEALKPANSFRIHTFIATSALHMEKKLRMTPDQVFEQAIQAVRFARQFTDDIEFSPE 141 ********************************************************************* PP TIGR00973 139 dagrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGla 207 d +r++++fl+rv+e +i+ Gattin+PdtvGya+P+ y+ li++++e++Pn dkai svhch+dlG+a lcl|FitnessBrowser__Cup4G11:RR42_RS05465 142 DGSRSDMDFLCRVLEGVIKEGATTINLPDTVGYAVPEGYAGLIRSVRERIPNSDKAIWSVHCHNDLGMA 210 ********************************************************************* PP TIGR00973 208 vanslaavkn.GarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltg 275 vanslaavk GarqvectinG+GeraGn++leevvma+k+r+d++++++g++t +i +s+lvs++tg lcl|FitnessBrowser__Cup4G11:RR42_RS05465 211 VANSLAAVKLgGARQVECTINGLGERAGNTSLEEVVMAVKTRRDYFDMDVGVDTTQIVPASKLVSQITG 279 ********9637********************************************************* PP TIGR00973 276 mlvqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfk 344 +vq+nka+vG+nafah sGihqdGvlk + tyei+++e++G +++k+vlgk sGr+a+k+rl+elG++ lcl|FitnessBrowser__Cup4G11:RR42_RS05465 280 FVVQPNKAVVGANAFAHASGIHQDGVLKARDTYEIMRAEDVGWSANKIVLGKLSGRNAFKQRLQELGIE 348 ********************************************************************* PP TIGR00973 345 ldee.eldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvk 412 l++e e++ +f++fkelad+k e+fded++a+v++e + + +e++++ +l+ +s + + p a v ++++ lcl|FitnessBrowser__Cup4G11:RR42_RS05465 349 LESEgEVNAAFTRFKELADQKSEIFDEDIMAIVSDEAH-DVNEHFRFISLSQHSETGERPHARVVFNMD 416 875549******************************98.78888************************* PP TIGR00973 413 geekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvatdi 481 g+e + GnGpvda+++aie + +l+ ys++a + g++a+gev+v+l g+ ++G+g + di lcl|FitnessBrowser__Cup4G11:RR42_RS05465 417 GNEVTGEGEGNGPVDATLHAIEGKVASGAELVLYSVNAITAGTQAQGEVTVRLSKGGRIVNGVGTDPDI 485 ********************************************************************* PP TIGR00973 482 veasakayvnaln 494 v asakay+ aln lcl|FitnessBrowser__Cup4G11:RR42_RS05465 486 VAASAKAYLAALN 498 ***********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (494 nodes) Target sequences: 1 (512 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.59 // [ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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