Align fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 17979 b3940 bifunctional aspartate kinase II/homoserine dehydrogenase II (NCBI)
Query= ecocyc::ASPKINIIHOMOSERDEHYDROGII-MONOMER (810 letters) >FitnessBrowser__Keio:17979 Length = 810 Score = 1596 bits (4132), Expect = 0.0 Identities = 810/810 (100%), Positives = 810/810 (100%) Query: 1 MSVIAQAGAKGRQLHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINW 60 MSVIAQAGAKGRQLHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINW Sbjct: 1 MSVIAQAGAKGRQLHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINW 60 Query: 61 LKLSQTDRLSAHQVQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLDSGINDA 120 LKLSQTDRLSAHQVQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLDSGINDA Sbjct: 61 LKLSQTDRLSAHQVQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLDSGINDA 120 Query: 121 VYAEVVGHGEVWSARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLL 180 VYAEVVGHGEVWSARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLL Sbjct: 121 VYAEVVGHGEVWSARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLL 180 Query: 181 VQHPGKRLVVTGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADP 240 VQHPGKRLVVTGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADP Sbjct: 181 VQHPGKRLVVTGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADP 240 Query: 241 RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIER 300 RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIER Sbjct: 241 RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIER 300 Query: 301 VLASGTGARIVTSHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLL 360 VLASGTGARIVTSHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLL Sbjct: 301 VLASGTGARIVTSHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLL 360 Query: 361 QFCYTSEVADSALKILDEAGLPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPV 420 QFCYTSEVADSALKILDEAGLPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPV Sbjct: 361 QFCYTSEVADSALKILDEAGLPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPV 420 Query: 421 EFTWQSDDGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFARE 480 EFTWQSDDGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFARE Sbjct: 421 EFTWQSDDGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFARE 480 Query: 481 QSTLSARTGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPY 540 QSTLSARTGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPY Sbjct: 481 QSTLSARTGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPY 540 Query: 541 DDLVVLDVTASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYN 600 DDLVVLDVTASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYN Sbjct: 541 DDLVVLDVTASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYN 600 Query: 601 ATVGAGLPINHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLT 660 ATVGAGLPINHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLT Sbjct: 601 ATVGAGLPINHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLT 660 Query: 661 EPDPRDDLSGKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNE 720 EPDPRDDLSGKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNE Sbjct: 661 EPDPRDDLSGKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNE 720 Query: 721 QMVQRLEAAREMGLVLRYVARFDANGKARVGVEAVREDHPLASLLPCDNVFAIESRWYRD 780 QMVQRLEAAREMGLVLRYVARFDANGKARVGVEAVREDHPLASLLPCDNVFAIESRWYRD Sbjct: 721 QMVQRLEAAREMGLVLRYVARFDANGKARVGVEAVREDHPLASLLPCDNVFAIESRWYRD 780 Query: 781 NPLVIRGPGAGRDVTAGAIQSDINRLAQLL 810 NPLVIRGPGAGRDVTAGAIQSDINRLAQLL Sbjct: 781 NPLVIRGPGAGRDVTAGAIQSDINRLAQLL 810 Lambda K H 0.320 0.135 0.397 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: 2176 Number of extensions: 49 Number of successful extensions: 1 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: 810 Length of database: 810 Length adjustment: 41 Effective length of query: 769 Effective length of database: 769 Effective search space: 591361 Effective search space used: 591361 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 56 (26.2 bits)
Align candidate 17979 b3940 (bifunctional aspartate kinase II/homoserine dehydrogenase II (NCBI))
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))
# 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/TIGR00657.hmm # target sequence database: /tmp/gapView.5418.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00657 [M=442] Accession: TIGR00657 Description: asp_kinases: aspartate kinase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-67 212.3 0.0 8.8e-67 212.0 0.0 1.1 1 lcl|FitnessBrowser__Keio:17979 b3940 bifunctional aspartate kin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17979 b3940 bifunctional aspartate kinase II/homoserine dehydrogenase II (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 212.0 0.0 8.8e-67 8.8e-67 6 441 .. 15 453 .. 12 454 .. 0.87 Alignments for each domain: == domain 1 score: 212.0 bits; conditional E-value: 8.8e-67 TIGR00657 6 qKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhlealeelas 82 KFGG+S+++v+ +va i+ + ++ + + VvSA +++T++L++ + + ++ +++ +++r+ + + ++ l + lcl|FitnessBrowser__Keio:17979 15 HKFGGSSLADVKCYLRVAGIMAEYSQPD--DMMVVSAAGSTTNQLINWLKLSQTDRLsaHQVQQTLRRYQCDLISGLLP 91 6*******************99999776..78899**************999998877755666666667676666664 PP TIGR00657 83 qalkeklkallekeleevkk..........ereldlilsvGEklSaallaaaleelgvkavsllgaeagiltdsefgrA 151 e+ +l+ + + +++ ++ +++++ +GE Sa+l++a+l+++g +++l+a++ ++++++ + lcl|FitnessBrowser__Keio:17979 92 A---EEADSLISAFVSDLERlaalldsginDAVYAEVVGHGEVWSARLMSAVLNQQG-LPAAWLDAREFLRAERAAQPQ 166 3...33333333333333333336677999***************************.888899********9998877 PP TIGR00657 152 kvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAdeveiytDVdGiytaDPrivp 228 + e + l++ll + + vv+GFi ++ ge+++LGR+GSD++A+ ++a+ + ++v i+ DV G+y+aDPr+v+ lcl|FitnessBrowser__Keio:17979 167 V-DEGLSYPLLQQLLVQHpgKRLVVTGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADPRKVK 244 7.8999999999998877779********************************************************** PP TIGR00657 229 eArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvs 307 +A +l+ + +Ea+ELa+l a vLh rtl+p+ ++i++ + ++ p+++ T i s ++ +++ d + ++ lcl|FitnessBrowser__Keio:17979 245 DACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIERVLASGTGARIVTSHDDVCLIEFQ 323 ************************************************999****998877777777777777777777 PP TIGR00657 308 vsgttmkpgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellkkkvkeekaleevevekklalvslvG 386 v +++ + +e+ ++l++a+v ++ ++++ ++f+ e ad+a ++l +e+ +e+++ ++lalv++vG lcl|FitnessBrowser__Keio:17979 324 VPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLLQFCYTSEVADSALKIL----DEAGLPGELRLRQGLALVAMVG 398 77777779999******************8888878***************96....6899999*************** PP TIGR00657 387 agmksapgvaakifeaLaeeniniemissseikisvvvdekdaekavealheklv 441 ag+ +p ++ ++L+ + + s i+++ v + e +++ lh+ ++ lcl|FitnessBrowser__Keio:17979 399 AGVTRNPLHCHRFWQQLKGQPVEFTWQSDDGISLVAVLRTGPTESLIQGLHQSVF 453 *******************777777666777777778888889999999999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (810 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: 00:00:00.03 # Mc/sec: 11.24 // [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