Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_028988888.1 G579_RS0102250 2-isopropylmalate synthase
Query= BRENDA::Q9JZG1 (517 letters) >NCBI__GCF_000423825.1:WP_028988888.1 Length = 510 Score = 651 bits (1679), Expect = 0.0 Identities = 331/509 (65%), Positives = 406/509 (79%), Gaps = 1/509 (0%) Query: 4 TNRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAI 63 + +IIFDTTLRDGEQSPGAAMT+++KIR+A+ LE+L VD+IEAGF AAS GDFEAV A+ Sbjct: 2 SEHLIIFDTTLRDGEQSPGAAMTRDDKIRIAKALERLRVDVIEAGFPAASNGDFEAVRAV 61 Query: 64 AKTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEA 123 A+ + S +C L+RA E+DI +AGEA+ PA RIHTFIATSPIHM+ KL+M P+QV+EA Sbjct: 62 AEAVKDSRICGLARAREQDITRAGEALKPAAANRIHTFIATSPIHMQAKLRMSPEQVLEA 121 Query: 124 AVKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTE 183 AV AVK+AR + +DVEFS EDA RS+ DFL + AVIEAGA TINIPDTVGY++P + Sbjct: 122 AVAAVKLARRFVEDVEFSPEDAGRSDEDFLCRVIEAVIEAGARTINIPDTVGYNLPDRFG 181 Query: 184 EFFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASV 243 R L + PN K V+S HCHNDLGLAVANSLAA++ GARQVECT+NGLGERAGNA++ Sbjct: 182 RLIRNLRERIPNADKAVFSVHCHNDLGLAVANSLAAVQNGARQVECTINGLGERAGNAAL 241 Query: 244 EEIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQ 303 EEIVMA++ R DLF +T IDTTQIVP+SKLVS+ITG+PVQPNKAIVGANAF+HESGIHQ Sbjct: 242 EEIVMAVRTRRDLFTCDTRIDTTQIVPASKLVSSITGFPVQPNKAIVGANAFAHESGIHQ 301 Query: 304 DGVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARF 363 DGVLKHRETYEIM AE VGW+TNR+SLGKLSGR AF+++L +LGI L EE LN AFARF Sbjct: 302 DGVLKHRETYEIMRAEDVGWSTNRISLGKLSGRAAFRSRLQELGIAL-GEEELNLAFARF 360 Query: 364 KELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEKR 423 K+LAD+K EIFDEDL AL+S E+ + E Y+ ++ +E G P A + + G EK Sbjct: 361 KDLADRKAEIFDEDLQALISTEVHAGLTEHYRLGYLRVCSEMGTRPEATVELLVDGVEKT 420 Query: 424 ASATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGA 483 A A G GPVDA FKAIES+AQSGA L +YSVNA+T GT++QGE +VRL + R VNGQGA Sbjct: 421 ARAHGGGPVDAAFKAIESIAQSGATLLLYSVNAITTGTDAQGEVTVRLEKDGRAVNGQGA 480 Query: 484 DTDVLVATAKAYLSALSKLEFSAAKPKAQ 512 DTD+++A+AKAYL+AL++L A+ Q Sbjct: 481 DTDIVIASAKAYLNALNRLAQPIARQHPQ 509 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: 685 Number of extensions: 20 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: 510 Length adjustment: 35 Effective length of query: 482 Effective length of database: 475 Effective search space: 228950 Effective search space used: 228950 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_028988888.1 G579_RS0102250 (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.25860.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-226 737.5 2.1 3.5e-226 737.3 2.1 1.0 1 lcl|NCBI__GCF_000423825.1:WP_028988888.1 G579_RS0102250 2-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028988888.1 G579_RS0102250 2-isopropylmalate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 737.3 2.1 3.5e-226 3.5e-226 2 494 .] 5 497 .. 4 497 .. 1.00 Alignments for each domain: == domain 1 score: 737.3 bits; conditional E-value: 3.5e-226 TIGR00973 2 vlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvgl 70 ++ifdttlrdGeq+pga++t ++k++iakalerl vd+ieaGfp++s+gdfeav+ +a++vk++r++gl lcl|NCBI__GCF_000423825.1:WP_028988888.1 5 LIIFDTTLRDGEQSPGAAMTRDDKIRIAKALERLRVDVIEAGFPAASNGDFEAVRAVAEAVKDSRICGL 73 68******************************************************************* PP TIGR00973 71 aravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaed 139 ara e+di a ealkpa+++rihtfiats+ih++akl+++ ++vle +v+avk a+ fv+dvefs+ed lcl|NCBI__GCF_000423825.1:WP_028988888.1 74 ARAREQDITRAGEALKPAAANRIHTFIATSPIHMQAKLRMSPEQVLEAAVAAVKLARRFVEDVEFSPED 142 ********************************************************************* PP TIGR00973 140 agrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlav 208 agr++ +fl+rv+ea+ieaGa tiniPdtvGy lP+ +g li++l+e++Pn dka++svhch+dlGlav lcl|NCBI__GCF_000423825.1:WP_028988888.1 143 AGRSDEDFLCRVIEAVIEAGARTINIPDTVGYNLPDRFGRLIRNLRERIPNADKAVFSVHCHNDLGLAV 211 ********************************************************************* PP TIGR00973 209 anslaavknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgml 277 anslaav+nGarqvectinG+GeraGnaalee+vma+++r+d++ +t i+t +i +s+lvs +tg + lcl|NCBI__GCF_000423825.1:WP_028988888.1 212 ANSLAAVQNGARQVECTINGLGERAGNAALEEIVMAVRTRRDLFTCDTRIDTTQIVPASKLVSSITGFP 280 ********************************************************************* PP TIGR00973 278 vqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkld 346 vq+nkaivG+nafahesGihqdGvlk++etyei+++e++G +++++ lgk sGraa+++rl+elG+ l lcl|NCBI__GCF_000423825.1:WP_028988888.1 281 VQPNKAIVGANAFAHESGIHQDGVLKHRETYEIMRAEDVGWSTNRISLGKLSGRAAFRSRLQELGIALG 349 ********************************************************************* PP TIGR00973 347 eeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkgee 415 eeel+ +f +fk+lad+k e+fdedl+al+++e++ +e+++l +l+v s + p atv+l v+g e lcl|NCBI__GCF_000423825.1:WP_028988888.1 350 EEELNLAFARFKDLADRKAEIFDEDLQALISTEVHAGLTEHYRLGYLRVCSEMGTRPEATVELLVDGVE 418 ********************************************************************* PP TIGR00973 416 keaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvatdivea 484 k+a a G Gpvda +kaie i + ll ys++a ++g+da+gev+v+le +g+ ++G+g++tdiv a lcl|NCBI__GCF_000423825.1:WP_028988888.1 419 KTARAHGGGPVDAAFKAIESIAQSGATLLLYSVNAITTGTDAQGEVTVRLEKDGRAVNGQGADTDIVIA 487 ********************************************************************* PP TIGR00973 485 sakayvnaln 494 sakay+naln lcl|NCBI__GCF_000423825.1:WP_028988888.1 488 SAKAYLNALN 497 *********9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (494 nodes) Target sequences: 1 (510 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.89 // [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