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)
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