Align fused aspartate kinase/homoserine dehydrogenase 2 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_008807866.1 KVAR_RS25005 bifunctional aspartate kinase/homoserine dehydrogenase II
Query= ecocyc::ASPKINIIHOMOSERDEHYDROGII-MONOMER (810 letters) >NCBI__GCF_000025465.1:WP_008807866.1 Length = 810 Score = 1475 bits (3818), Expect = 0.0 Identities = 737/810 (90%), Positives = 779/810 (96%) Query: 1 MSVIAQAGAKGRQLHKFGGSSLADVKCYLRVAGIMAEYSQPDDMMVVSAAGSTTNQLINW 60 MSVIAQAGAKGRQLHKFGGSSLAD KCYLRVAGIM EYSQ DMMVVSAAGSTTNQLI+W Sbjct: 1 MSVIAQAGAKGRQLHKFGGSSLADAKCYLRVAGIMKEYSQAGDMMVVSAAGSTTNQLISW 60 Query: 61 LKLSQTDRLSAHQVQQTLRRYQCDLISGLLPAEEADSLISAFVSDLERLAALLDSGINDA 120 LKLSQ+DRL+AHQVQQ+LRRYQ +LI GL+ AD+LI+AF+ DLERLA LLD G+ +A Sbjct: 61 LKLSQSDRLAAHQVQQSLRRYQTELIGGLVEPAAADTLIAAFIHDLERLAGLLDGGVTEA 120 Query: 121 VYAEVVGHGEVWSARLMSAVLNQQGLPAAWLDAREFLRAERAAQPQVDEGLSYPLLQQLL 180 VYAEVVGHGEVWSARLM+AVLNQ G+ AAWLDAR FLRAERAAQPQVDEGLSYPLLQQL+ Sbjct: 121 VYAEVVGHGEVWSARLMAAVLNQLGMEAAWLDARAFLRAERAAQPQVDEGLSYPLLQQLM 180 Query: 181 VQHPGKRLVVTGFISRNNAGETVLLGRNGSDYSATQIGALAGVSRVTIWSDVAGVYSADP 240 QHP KRLVVTGFISRN AGETVLLGRNGSDYSATQIGALAG SRVTIWSDVAGVYSADP Sbjct: 181 AQHPNKRLVVTGFISRNQAGETVLLGRNGSDYSATQIGALAGASRVTIWSDVAGVYSADP 240 Query: 241 RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSGSEIDLQLRCSYTPDQGSTRIER 300 RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVS S+IDLQLRCSYTP+QGSTRIER Sbjct: 241 RKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSASDIDLQLRCSYTPEQGSTRIER 300 Query: 301 VLASGTGARIVTSHDDVCLIEFQVPASQDFKLAHKEIDQILKRAQVRPLAVGVHNDRQLL 360 VLASGTGARIVTSHDDVCL+EFQVPAS DFKLAHKE+D +LKRAQ+RPLAVGVH DR+LL Sbjct: 301 VLASGTGARIVTSHDDVCLVEFQVPASHDFKLAHKELDALLKRAQLRPLAVGVHADRKLL 360 Query: 361 QFCYTSEVADSALKILDEAGLPGELRLRQGLALVAMVGAGVTRNPLHCHRFWQQLKGQPV 420 QFCYTSEVADSALK+LDEAGLPGELRLRQ LALVAMVGAGVTRNPLHCHRFWQQLKGQPV Sbjct: 361 QFCYTSEVADSALKLLDEAGLPGELRLRQKLALVAMVGAGVTRNPLHCHRFWQQLKGQPV 420 Query: 421 EFTWQSDDGISLVAVLRTGPTESLIQGLHQSVFRAEKRIGLVLFGKGNIGSRWLELFARE 480 EFTWQS++GISLVAVLR GPTESLIQGLHQ++FRAEKRIGL+LFGKGNIGSRWLELFARE Sbjct: 421 EFTWQSEEGISLVAVLRAGPTESLIQGLHQTLFRAEKRIGLMLFGKGNIGSRWLELFARE 480 Query: 481 QSTLSARTGFEFVLAGVVDSRRSLLSYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPY 540 Q+TLSARTGFEFVLAGVVDS+RSLL+YDGLDASRALAFFNDEAVEQDEESLFLWMRAHPY Sbjct: 481 QTTLSARTGFEFVLAGVVDSKRSLLNYDGLDASRALAFFNDEAVEQDEESLFLWMRAHPY 540 Query: 541 DDLVVLDVTASQQLADQYLDFASHGFHVISANKLAGASDSNKYRQIHDAFEKTGRHWLYN 600 DDLVVLDVTAS+QLADQYLDFASHGFHVISANKLAGAS S+KYRQIHDAFEKTGRHWLYN Sbjct: 541 DDLVVLDVTASEQLADQYLDFASHGFHVISANKLAGASSSDKYRQIHDAFEKTGRHWLYN 600 Query: 601 ATVGAGLPINHTVRDLIDSGDTILSISGIFSGTLSWLFLQFDGSVPFTELVDQAWQQGLT 660 ATVGAGLP+NHTVRDLIDSGDTIL +SGIFSGTLSWLFLQFDG+VPFT+LVDQAWQQGLT Sbjct: 601 ATVGAGLPVNHTVRDLIDSGDTILGLSGIFSGTLSWLFLQFDGTVPFTDLVDQAWQQGLT 660 Query: 661 EPDPRDDLSGKDVMRKLVILAREAGYNIEPDQVRVESLVPAHCEGGSIDHFFENGDELNE 720 EPDPR DLSGKDVMRKLVILAREAGY+IEPDQVRVESLVPAHCE GS+DHFFENG+ELNE Sbjct: 661 EPDPRVDLSGKDVMRKLVILAREAGYDIEPDQVRVESLVPAHCEEGSVDHFFENGEELNE 720 Query: 721 QMVQRLEAAREMGLVLRYVARFDANGKARVGVEAVREDHPLASLLPCDNVFAIESRWYRD 780 QM+QRLEAAREMGLVLRYVARFDANGKARVGVEAVRE+HPLA+LLPCDNVFAIESRWYRD Sbjct: 721 QMLQRLEAAREMGLVLRYVARFDANGKARVGVEAVREEHPLAALLPCDNVFAIESRWYRD 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: 2058 Number of extensions: 47 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 WP_008807866.1 KVAR_RS25005 (bifunctional aspartate kinase/homoserine dehydrogenase II)
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.3870410.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-69 220.4 0.0 3.1e-69 220.1 0.0 1.1 1 NCBI__GCF_000025465.1:WP_008807866.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000025465.1:WP_008807866.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 220.1 0.0 3.1e-69 3.1e-69 6 441 .. 15 453 .. 12 454 .. 0.86 Alignments for each domain: == domain 1 score: 220.1 bits; conditional E-value: 3.1e-69 TIGR00657 6 qKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhlea 76 KFGG+S+++++ +va i+k+ ++ g + VvSA +++T++L++ + +s++ +++ + +r+ + e NCBI__GCF_000025465.1:WP_008807866.1 15 HKFGGSSLADAKCYLRVAGIMKEYSQAG--DMMVVSAAGSTTNQLISWLKLSQSDRLaaHQVQQSLRRYQTEL 85 6**********************99998..67899****************9999976555555666666666 PP TIGR00657 77 leela.sqalkeklkallekeleevkk..........ereldlilsvGEklSaallaaaleelgvkavsllga 138 + l + + +l+++ ++ +++ e+ +++++ +GE Sa+l+aa+l++lg ++++l+a NCBI__GCF_000025465.1:WP_008807866.1 86 IGGLVeP----AAADTLIAAFIHDLERlaglldggvtEAVYAEVVGHGEVWSARLMAAVLNQLG-MEAAWLDA 153 6666634....44444455555554445557889******************************.778899** PP TIGR00657 139 eagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGGSDltAallAaalkAde 209 +a ++++++ + + e + l++l+ + + vv+GFi ++ ge+++LGR+GSD++A+ ++a+ +A++ NCBI__GCF_000025465.1:WP_008807866.1 154 RAFLRAERAAQPQV-DEGLSYPLLQQLMAQHpnKRLVVTGFISRNQAGETVLLGRNGSDYSATQIGALAGASR 225 ******99887777.88888888888877767799************************************** PP TIGR00657 210 veiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTli 282 v i+ DV G+y+aDPr+v++A +l+ + +Ea+ELa+l a vLh rtl+p+ +++i++ + ++ pe++ T i NCBI__GCF_000025465.1:WP_008807866.1 226 VTIWSDVAGVYSADPRKVKDACLLPLLRLDEASELARLAAPVLHARTLQPVSASDIDLQLRCSYTPEQGSTRI 298 *******************************************************************999*** PP TIGR00657 283 vakskseeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssetsisfvvdkedadk 355 s ++ +++ d + ++v + + + +e+ l++a+ ++ ++++ ++f+ e ad+ NCBI__GCF_000025465.1:WP_008807866.1 299 ERVLASGTGARIVTSHDDVCLVEFQVPASHDFKLAHKELDALLKRAQLRPLAVGVHADRKLLQFCYTSEVADS 371 9998877766666666666666667776666699999*****************8888888************ PP TIGR00657 356 akellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemissseikisvvvdekd 428 a +ll +e+ +e+++ +klalv++vGag+ +p ++ ++L+ + + s i+++ v + NCBI__GCF_000025465.1:WP_008807866.1 372 ALKLL----DEAGLPGELRLRQKLALVAMVGAGVTRNPLHCHRFWQQLKGQPVEFTWQSEEGISLVAVLRAGP 440 ***96....6899999*********************************965555555555555556677888 PP TIGR00657 429 aekavealheklv 441 e +++ lh+ l+ NCBI__GCF_000025465.1:WP_008807866.1 441 TESLIQGLHQTLF 453 8999999999987 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 24.68 // [ok]
This GapMind analysis is from Jul 25 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