Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 351931 BT2403 aspartokinase/homoserine dehydrogenase (NCBI ptt file)
Query= reanno::Btheta:351931 (811 letters) >FitnessBrowser__Btheta:351931 Length = 811 Score = 1577 bits (4083), Expect = 0.0 Identities = 811/811 (100%), Positives = 811/811 (100%) Query: 1 MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE 60 MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE Sbjct: 1 MKVMKFGGTSVGSVNSILSVKRIVESAGEPVIVVVSALGGITDKLINTSKMAAAGDSAYE 60 Query: 61 GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV 120 GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV Sbjct: 61 GEFREIVYRHVEMIKEVIPAGAGQVALQRQIGELLNELKDIFQGIYLIRDLSPKTSDTIV 120 Query: 121 SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV 180 SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV Sbjct: 121 SYGERLSSIIVAELIDEAKWFDSRTFIKTEKKHNKHTIDADLTNQLVKEAFHSIPKVSLV 180 Query: 181 PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI 240 PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI Sbjct: 181 PGFISSDKVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTDVDGFMTADPRVISTAYTI 240 Query: 241 SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA 300 SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA Sbjct: 241 SELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQSKA 300 Query: 301 IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA 360 IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA Sbjct: 301 IKGISSINDTSLITVQGLGMVGVIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNA 360 Query: 361 DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI 420 DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI Sbjct: 361 DADLACEVLNEEFAKEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGI 420 Query: 421 NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI 480 NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI Sbjct: 421 NVIACAQGASETNISFVVDSKSLRKSLNVIHDSFFLSEYQVLNLFICGIGTVGGSLVEQI 480 Query: 481 RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG 540 RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG Sbjct: 481 RCQQQKLMMENGLKLHVVGIIDAAKAMFSREGFDLANFREELQKKGKDSNLQTIRDEIVG 540 Query: 541 MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY 600 MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY Sbjct: 541 MNIFNSVFVDCTASPDIASLYKDLLQHNVSVVAANKIAASSAYENYRELKTIARQRGVKY 600 Query: 601 LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE 660 LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE Sbjct: 601 LFETNVGAGLPIINTINDLIHSGDKILKIEAVLSGTLNYIFNKISADIPFSRTIKMAQEE 660 Query: 661 RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFEGSLDDFWKRVPS 720 RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFEGSLDDFWKRVPS Sbjct: 661 RYSEPDPRIDLSGKDVIRKLVILAREAGYHIEQEDVEKNLFVPNDFFEGSLDDFWKRVPS 720 Query: 721 LDADFEARRQVLEKEHKHWRFVAKLEDGKASVGLQEVGANHPFYGLEGSNNIILLTTERY 780 LDADFEARRQVLEKEHKHWRFVAKLEDGKASVGLQEVGANHPFYGLEGSNNIILLTTERY Sbjct: 721 LDADFEARRQVLEKEHKHWRFVAKLEDGKASVGLQEVGANHPFYGLEGSNNIILLTTERY 780 Query: 781 KEYPMMIQGYGAGAGVTAAGVFADIMSIANV 811 KEYPMMIQGYGAGAGVTAAGVFADIMSIANV Sbjct: 781 KEYPMMIQGYGAGAGVTAAGVFADIMSIANV 811 Lambda K H 0.317 0.135 0.377 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: 1908 Number of extensions: 45 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: 811 Length of database: 811 Length adjustment: 41 Effective length of query: 770 Effective length of database: 770 Effective search space: 592900 Effective search space used: 592900 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 bits)
Align candidate 351931 BT2403 (aspartokinase/homoserine dehydrogenase (NCBI ptt file))
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.20778.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.7e-115 370.4 4.6 1.1e-114 369.9 4.6 1.2 1 lcl|FitnessBrowser__Btheta:351931 BT2403 aspartokinase/homoserine Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:351931 BT2403 aspartokinase/homoserine dehydrogenase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 369.9 4.6 1.1e-114 1.1e-114 5 441 .. 3 455 .. 1 456 [. 0.94 Alignments for each domain: == domain 1 score: 369.9 bits; conditional E-value: 1.1e-114 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee..keliekirekhleale 78 V+KFGGtSvg+v++i v +iv+++ ++v+VVvSA +g+Td+L+++++ + +++ + + ++i ++h+e ++ lcl|FitnessBrowser__Btheta:351931 3 VMKFGGTSVGSVNSILSVKRIVESAG---EPVIVVVSALGGITDKLINTSKMAAAGDSayEGEFREIVYRHVEMIK 75 9***************9988887765...79************************9998878899*********** PP TIGR00657 79 ela.sqalkeklkallekeleevkk............ereldlilsvGEklSaallaaaleelgvkavsllgaeag 141 e++ a + l++ + + l+e+k +++ d+i+s+GE+lS+ ++a+++ e +++++ lcl|FitnessBrowser__Btheta:351931 76 EVIpAGAGQVALQRQIGELLNELKDifqgiylirdlsPKTSDTIVSYGERLSSIIVAELIDEAK-----WFDSRTF 146 ***888999999999999999999999********************************98887.....******* PP TIGR00657 142 iltdsefgrAkvleeikterleklleeg.iivvvaGFiGat.ekgeittLGRGGSDltAallAaalkAdeveiytD 215 i t++++++ + ++ +++ ++++ + ++ +v GFi ++ +g++t LGRGGSD+tAa++Aaal+A+ +ei+tD lcl|FitnessBrowser__Btheta:351931 147 IKTEKKHNKHTIDADLTNQLVKEAFHSIpKVSLVPGFISSDkVSGDVTNLGRGGSDYTAAIIAAALDASSLEIWTD 222 ***********666666666666666557***********9679******************************** PP TIGR00657 216 VdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpeaeGTlivakskseee 291 VdG +taDPr++++A + e+sy Ea EL ++Gakv +p t+ p+ +++ipi++k+tfnp++ GT+i +++++ ++ lcl|FitnessBrowser__Btheta:351931 223 VDGFMTADPRVISTAYTISELSYVEATELCNFGAKVVYPPTIYPVCHKNIPIIIKNTFNPDGVGTVIKQETSNPQS 298 ************************************************************************9999 PP TIGR00657 292 pavkalsldknqalvsvsgttmk..pgilaevfgalaeakvnvdlilqsssetsisfvvdkedadkakellk...k 362 +a+k++s+ ++ +l++v+g +m g+ ++f+ala+++++v+l++q sse+s s+ v + dad a e+l+ lcl|FitnessBrowser__Btheta:351931 299 KAIKGISSINDTSLITVQGLGMVgvIGVNYRIFKALAKNGISVFLVSQASSENSTSIGVRNADADLACEVLNeefA 374 ***********************9999*******************************************995554 PP TIGR00657 363 kvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeniniemis..sseikisvvvdekdaekaveal 436 k+ e +++++ e++la+v++vG++mk++pg+a+k+f +L +++in+ + + +se++is+vvd+k k ++++ lcl|FitnessBrowser__Btheta:351931 375 KEIEMGEISPILAERNLATVAIVGENMKHTPGIAGKLFGTLGRNGINVIACAqgASETNISFVVDSKSLRKSLNVI 450 5566667788889***********************************99999*********************** PP TIGR00657 437 heklv 441 h+ ++ lcl|FitnessBrowser__Btheta:351931 451 HDSFF 455 **997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (811 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 19.26 // [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