Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate CA265_RS23475 CA265_RS23475 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Pedo557:CA265_RS23475 (817 letters) >FitnessBrowser__Pedo557:CA265_RS23475 Length = 817 Score = 1590 bits (4118), Expect = 0.0 Identities = 817/817 (100%), Positives = 817/817 (100%) Query: 1 MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMAERGEDY 60 MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMAERGEDY Sbjct: 1 MKVLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMAERGEDY 60 Query: 61 DTHLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTKDQIL 120 DTHLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTKDQIL Sbjct: 61 DTHLKEIEAKHFAVIRSLLPAAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTKDQIL 120 Query: 121 SYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQENKD 180 SYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQENKD Sbjct: 121 SYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQENKD 180 Query: 181 KVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADPRMVKK 240 KVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADPRMVKK Sbjct: 181 KVLFVTGFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADPRMVKK 240 Query: 241 AFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKSDVKAS 300 AFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKSDVKAS Sbjct: 241 AFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKSDVKAS 300 Query: 301 SLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSITFAV 360 SLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSITFAV Sbjct: 301 SLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSITFAV 360 Query: 361 KPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGRLFNALGR 420 KPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGRLFNALGR Sbjct: 361 KPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGRLFNALGR 420 Query: 421 NGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFFTDLKRTLNVFCLGTGNIGKTLF 480 NGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFFTDLKRTLNVFCLGTGNIGKTLF Sbjct: 421 NGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFFTDLKRTLNVFCLGTGNIGKTLF 480 Query: 481 NQLKEQMPFLAANNDLQVKVTGISNTRKMIFSADGLSLENWETELNTNGEPADLAGFVAK 540 NQLKEQMPFLAANNDLQVKVTGISNTRKMIFSADGLSLENWETELNTNGEPADLAGFVAK Sbjct: 481 NQLKEQMPFLAANNDLQVKVTGISNTRKMIFSADGLSLENWETELNTNGEPADLAGFVAK 540 Query: 541 MKALNLPNCVFVDNTAAESPIEFYQGIFESSISVVTCNKKGNSADYAQYKSFKDTARKFG 600 MKALNLPNCVFVDNTAAESPIEFYQGIFESSISVVTCNKKGNSADYAQYKSFKDTARKFG Sbjct: 541 MKALNLPNCVFVDNTAAESPIEFYQGIFESSISVVTCNKKGNSADYAQYKSFKDTARKFG 600 Query: 601 VDFYYETNVGAGLPIIRTLRELMMSGDKVARIEAILSGTISYIFNNFKGEAGFYETVKEA 660 VDFYYETNVGAGLPIIRTLRELMMSGDKVARIEAILSGTISYIFNNFKGEAGFYETVKEA Sbjct: 601 VDFYYETNVGAGLPIIRTLRELMMSGDKVARIEAILSGTISYIFNNFKGEAGFYETVKEA 660 Query: 661 QELGYTEPDPRDDLNGKDFMRKMLILARDAGYPLEASDVKIDNILPEACLNASSVEDFYS 720 QELGYTEPDPRDDLNGKDFMRKMLILARDAGYPLEASDVKIDNILPEACLNASSVEDFYS Sbjct: 661 QELGYTEPDPRDDLNGKDFMRKMLILARDAGYPLEASDVKIDNILPEACLNASSVEDFYS 720 Query: 721 ELQANAAYFENLKQTAANDGKVLRYIGKLEDGNVEISLQMVDDSHPFYMLSGSDNIISFT 780 ELQANAAYFENLKQTAANDGKVLRYIGKLEDGNVEISLQMVDDSHPFYMLSGSDNIISFT Sbjct: 721 ELQANAAYFENLKQTAANDGKVLRYIGKLEDGNVEISLQMVDDSHPFYMLSGSDNIISFT 780 Query: 781 TDRYKSRPLVVKGPGAGAEVTAAGVFADIINVGTLNK 817 TDRYKSRPLVVKGPGAGAEVTAAGVFADIINVGTLNK Sbjct: 781 TDRYKSRPLVVKGPGAGAEVTAAGVFADIINVGTLNK 817 Lambda K H 0.316 0.133 0.369 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: 2185 Number of extensions: 73 Number of successful extensions: 3 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: 817 Length of database: 817 Length adjustment: 41 Effective length of query: 776 Effective length of database: 776 Effective search space: 602176 Effective search space used: 602176 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 (21.6 bits) S2: 56 (26.2 bits)
Align candidate CA265_RS23475 CA265_RS23475 (bifunctional aspartate kinase/homoserine dehydrogenase I)
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.23065.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.7e-126 406.3 1.2 1.2e-125 405.9 1.2 1.1 1 lcl|FitnessBrowser__Pedo557:CA265_RS23475 CA265_RS23475 bifunctional aspar Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS23475 CA265_RS23475 bifunctional aspartate kinase/homoserine dehydrogenase I # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.9 1.2 1.2e-125 1.2e-125 5 441 .. 3 458 .. 1 459 [. 0.93 Alignments for each domain: == domain 1 score: 405.9 bits; conditional E-value: 1.2e-125 TIGR00657 5 VqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseee.keliekire 71 V+KFGGtSvg++e+ik + ++v +ek+k+ ++vVV+SAm+gvT+ L e+ae ++++e+ + +++i++ lcl|FitnessBrowser__Pedo557:CA265_RS23475 3 VLKFGGTSVGSAENIKTLLRLVGEEKQKN-SPVVVLSAMSGVTNLLTEMAEMAERGEDyDTHLKEIEA 69 89************************777.9**************************98889****** PP TIGR00657 72 khlealeelasqalkeklkallekeleevkk............ereldlilsvGEklSaallaaalee 127 kh++ + +l + a ++ + + l+ ++e++ +++d ils+GE+ S+ +++ + ++ lcl|FitnessBrowser__Pedo557:CA265_RS23475 70 KHFAVIRSLLPAAAQNPVFTRLKIFFNELEDllqavanlrelsLQTKDQILSYGERCSTFMISHIASK 137 *******9998888887777777777777767778*******9999************9888776655 PP TIGR00657 128 lgvkavsllgaeagiltdsefgrAkvleeikterleklleeg..iivvvaGFiGatekgeittLGRGG 193 + + ++++ i tds+fg+Akv +e ++ ++++ +e+ ++ v+GFi+++ g++ttLGRGG lcl|FitnessBrowser__Pedo557:CA265_RS23475 138 N-IGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQENkdKVLFVTGFIASNAAGRVTTLGRGG 204 4.467778888999***********88888888889999988899*********************** PP TIGR00657 194 SDltAallAaalkAdeveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepam 261 SD+tAa+ +aal+A+e+ei+tDV+G +taDPr+v++A l+e+sy Ea+EL+++Gakv++p t+ pa lcl|FitnessBrowser__Pedo557:CA265_RS23475 205 SDYTAAVWGAALNAEEIEIWTDVNGMMTADPRMVKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAF 272 ******************************************************************** PP TIGR00657 262 rakipivvkstfnpeaeGTlivakskseeepavkalsldknqalvsvsgttmk..pgilaevfgalae 327 +kipiv+k+tf+p+ GT i ++ k ++ ++k++s+ ++ +++++ g++m +g+ ++f+ l++ lcl|FitnessBrowser__Pedo557:CA265_RS23475 273 MKKIPIVIKNTFEPDFAGTYIKSDVKASS-LPIKGISSIDHISIINLTGSGMVgkAGFSGRLFSLLSR 339 ************************99666.**********************999************* PP TIGR00657 328 akvnvdlilqsssetsisfvvdkedadkakellk...kkvkeekaleevevekklalvslvGagmksa 392 +++nv+li+qssse+si+f+v+ +da++a +l k + ++++k+le eve++la+ ++vG++mk + lcl|FitnessBrowser__Pedo557:CA265_RS23475 340 EQINVVLITQSSSEHSITFAVKPTDASQAISLIKkefELELDAKKLELPEVENNLAVLAIVGENMKRT 407 ********************************9966655667777777789***************** PP TIGR00657 393 pgvaakifeaLaeeniniemis..sseikisvvvdekdaekavealheklv 441 pg+ +++f+aL +++in+++i+ sse++isv+++++d kav+a+h++++ lcl|FitnessBrowser__Pedo557:CA265_RS23475 408 PGMSGRLFNALGRNGINVRAIAqgSSEYNISVIISKDDLSKAVNAVHDAFF 458 *************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (817 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: 00:00:00.02 # Mc/sec: 17.89 // [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