Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_012969593.1 ALVIN_RS01770 2-isopropylmalate synthase
Query= BRENDA::Q9JZG1 (517 letters) >NCBI__GCF_000025485.1:WP_012969593.1 Length = 516 Score = 649 bits (1673), Expect = 0.0 Identities = 325/514 (63%), Positives = 406/514 (78%) Query: 1 MTQTNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAV 60 M+ + +IIFDTTLRDGEQSPGA+MT++EK+R+A+ LEKL VD+IEAGF ASPGDFEAV Sbjct: 1 MSAKDHLIIFDTTLRDGEQSPGASMTRDEKVRIAKALEKLRVDVIEAGFPIASPGDFEAV 60 Query: 61 NAIAKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQV 120 A+A+ + S VC L+RA++ DI +AGEA+ A RIHTFIATSPIHME KL+M P QV Sbjct: 61 KAVAEAVKDSRVCGLARALDADIDRAGEALKNANAGRIHTFIATSPIHMEKKLRMSPDQV 120 Query: 121 IEAAVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPY 180 +E AV AVK AR TDDVEFS EDA RSEIDFL I AVI+AGA T+NIPDTVGY+IP Sbjct: 121 LEQAVYAVKRARNLTDDVEFSPEDAGRSEIDFLCRILEAVIDAGARTLNIPDTVGYNIPD 180 Query: 181 KTEEFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGN 240 + L A+ PN K ++S HCHNDLGLAVANSLAA++ GARQVECT+NGLGERAGN Sbjct: 181 QFGSLIATLRARIPNADKAIFSVHCHNDLGLAVANSLAAVRNGARQVECTINGLGERAGN 240 Query: 241 ASVEEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESG 300 A++EEIVM ++ R DLF +T +DTTQI+ S+LVS ITG+ VQPNKA+VGANAF+HESG Sbjct: 241 AALEEIVMTVRTRQDLFDCDTRLDTTQIMNCSRLVSGITGFAVQPNKAVVGANAFAHESG 300 Query: 301 IHQDGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAF 360 IHQDGVLKHRETYEIM A+ VGW+ NR+ LGK SGRNAF+ +L +LG+ + SEE LNAAF Sbjct: 301 IHQDGVLKHRETYEIMRAQDVGWSENRMVLGKHSGRNAFRARLQELGVVMNSEEDLNAAF 360 Query: 361 ARFKELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGE 420 ARFK+LADKK EIFDEDL ALV++ E K +S ++ +ETGE P A +V ++ G+ Sbjct: 361 ARFKDLADKKHEIFDEDLQALVTETTLETANERVKLVSMRVCSETGETPSAALVLAVDGQ 420 Query: 421 EKRASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNG 480 E+ +ATG GPVDA FKAIES+ Q+G+ L++YSVNA+T GT++QGE +VRL +G R+VNG Sbjct: 421 ERSGTATGGGPVDATFKAIESLVQTGSTLKLYSVNAITSGTDAQGEVTVRLEKGGRIVNG 480 Query: 481 QGADTDVLVATAKAYLSALSKLEFSAAKPKAQGS 514 QGADTD+LVA+AKAY++A +K+ A + Q + Sbjct: 481 QGADTDILVASAKAYINACNKILHPAERAHPQAA 514 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: 707 Number of extensions: 21 Number of successful extensions: 2 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: 516 Length adjustment: 35 Effective length of query: 482 Effective length of database: 481 Effective search space: 231842 Effective search space used: 231842 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_012969593.1 ALVIN_RS01770 (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.26432.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-226 738.5 4.6 1.8e-226 738.3 4.6 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012969593.1 ALVIN_RS01770 2-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025485.1:WP_012969593.1 ALVIN_RS01770 2-isopropylmalate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 738.3 4.6 1.8e-226 1.8e-226 2 494 .] 7 500 .. 6 500 .. 0.99 Alignments for each domain: == domain 1 score: 738.3 bits; conditional E-value: 1.8e-226 TIGR00973 2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvgl 70 ++ifdttlrdGeq+pgas+t +ek++iakale+l vd+ieaGfp++s+gdfeav+ +a++vk++rv+gl lcl|NCBI__GCF_000025485.1:WP_012969593.1 7 LIIFDTTLRDGEQSPGASMTRDEKVRIAKALEKLRVDVIEAGFPIASPGDFEAVKAVAEAVKDSRVCGL 75 68******************************************************************* PP TIGR00973 71 aravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaed 139 ara++ did a ealk+a++ rihtfiats+ih+e+kl+++ d+vle++v+avk+a+n++ddvefs+ed lcl|NCBI__GCF_000025485.1:WP_012969593.1 76 ARALDADIDRAGEALKNANAGRIHTFIATSPIHMEKKLRMSPDQVLEQAVYAVKRARNLTDDVEFSPED 144 ********************************************************************* PP TIGR00973 140 agrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlav 208 agr+e++fl+r++ea+i+aGa t+niPdtvGy +P+++g+li++l+ ++Pn dkai+svhch+dlGlav lcl|NCBI__GCF_000025485.1:WP_012969593.1 145 AGRSEIDFLCRILEAVIDAGARTLNIPDTVGYNIPDQFGSLIATLRARIPNADKAIFSVHCHNDLGLAV 213 ********************************************************************* PP TIGR00973 209 anslaavknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgml 277 anslaav+nGarqvectinG+GeraGnaalee+vm +++r+d+++ +t ++t +i++ srlvs +tg + lcl|NCBI__GCF_000025485.1:WP_012969593.1 214 ANSLAAVRNGARQVECTINGLGERAGNAALEEIVMTVRTRQDLFDCDTRLDTTQIMNCSRLVSGITGFA 282 ********************************************************************* PP TIGR00973 278 vqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkl. 345 vq+nka+vG+nafahesGihqdGvlk++etyei++++++G +++++vlgk+sGr+a++ rl+elG+ + lcl|NCBI__GCF_000025485.1:WP_012969593.1 283 VQPNKAVVGANAFAHESGIHQDGVLKHRETYEIMRAQDVGWSENRMVLGKHSGRNAFRARLQELGVVMn 351 *****************************************************************8762 PP TIGR00973 346 deeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkge 414 +ee+l+ +f +fk+ladkk+e+fdedl+alv+e + + +e++kl++++v s + + p a++ l+v+g+ lcl|NCBI__GCF_000025485.1:WP_012969593.1 352 SEEDLNAAFARFKDLADKKHEIFDEDLQALVTETTLETANERVKLVSMRVCSETGETPSAALVLAVDGQ 420 6789***************************************************************** PP TIGR00973 415 ekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvatdive 483 e++ +atG Gpvda++kaie ++++ l+ ys++a ++g+da+gev+v+le g+ ++G+g++tdi+ lcl|NCBI__GCF_000025485.1:WP_012969593.1 421 ERSGTATGGGPVDATFKAIESLVQTGSTLKLYSVNAITSGTDAQGEVTVRLEKGGRIVNGQGADTDILV 489 ********************************************************************* PP TIGR00973 484 asakayvnaln 494 asakay+na n lcl|NCBI__GCF_000025485.1:WP_012969593.1 490 ASAKAYINACN 500 *********88 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (494 nodes) Target sequences: 1 (516 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: 11.64 // [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