Align aspartate kinase; homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 6936415 Sama_0603 aspartate kinase III (RefSeq)
Query= reanno::Pedo557:CA265_RS23475 (817 letters) >FitnessBrowser__SB2B:6936415 Length = 452 Score = 236 bits (601), Expect = 3e-66 Identities = 153/461 (33%), Positives = 257/461 (55%), Gaps = 22/461 (4%) Query: 3 VLKFGGTSVGSAENIKTLLRLVGEEKQKNSPVVVLSAMSGVTNLLTEMAEMAERGEDYDT 62 V KFGGTSV + +V +VV+SA SGVTNLL E+ + E Sbjct: 5 VAKFGGTSVADFNAMSRCAAIVLANSATR--LVVVSASSGVTNLLVELTQATVTDERRLQ 62 Query: 63 HLKEIEAKHFAVIRSLLP----AAAQNPVFTRLKIFFNELEDLLQAVANLRELSLQTKDQ 118 LK+I +A++ L AAA + + +R+ + L + S D+ Sbjct: 63 LLKQIAQIQYAILDKLERPQDVAAALDALLSRISVLSESL---------ILNRSKAIMDE 113 Query: 119 ILSYGERCSTFMISHIASKNIGDSIYVNGSDLIKTDSNFGQAKVETELTEMLINNFYQEN 178 +LS GE+CS + S + + S + +++TDS+FG+A+ + E L +F Q Sbjct: 114 LLSMGEQCSALLFSAVLRQQGAKSSSFDVRQVMRTDSHFGRAEPQIEDIAALARDFLQPL 173 Query: 179 KDKVLFVT-GFIASNAAGRVTTLGRGGSDYTAAVWGAALNAEEIEIWTDVNGMMTADPRM 237 ++ + VT GFI ++A GR TTLGRGGSDY+AA+ AL A+ +EIWTDV G+ T DPR+ Sbjct: 174 LERDIVVTQGFIGADAEGRTTTLGRGGSDYSAALLAEALRADAVEIWTDVAGIYTTDPRL 233 Query: 238 VKKAFSLPELSYTEAMELSYFGAKVIYPPTMIPAFMKKIPIVIKNTFEPDFAGTYIKSDV 297 A + E+S+ EA E++ FGAKV++P T++PA ++I + + ++ EP+ GT+I+ V Sbjct: 234 APNARPIAEISFNEAAEMATFGAKVLHPATILPAVRQQIQVFVGSSREPEKGGTWIRHQV 293 Query: 298 KASSLPIKGISSIDHISIINLTGSGMVGKAGFSGRLFSLLSREQINVVLITQSSSEHSIT 357 + + ++ +++NL M+ GF F+ L+R +I+V LIT +SE +++ Sbjct: 294 DNPPI-YRAVAVRRDQTLLNLHSLQMLHARGFLAETFATLARHKISVDLIT--TSEVNVS 350 Query: 358 FAVKPTDASQAISLIKKEFELELDAKKLELPEVENNLAVLAIVGENMKRTPGMSGRLFNA 417 + T + S + E L+ ++ + VE+NLA++AI+G + TPG+ ++F Sbjct: 351 LTLDKTGSDSTGSGLLSEALLQELSQHCRV-RVEDNLALVAIIGNRIASTPGICRQVFTV 409 Query: 418 LGRNGINVRAIAQGSSEYNISVIISKDDLSKAVNAVHDAFF 458 L + NVR I QG+S +N+ V++++ + ++ V A+H+ F Sbjct: 410 LENH--NVRMICQGASPHNLCVLVAESEAAQVVKALHENLF 448 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: 617 Number of extensions: 23 Number of successful extensions: 6 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: 452 Length adjustment: 37 Effective length of query: 780 Effective length of database: 415 Effective search space: 323700 Effective search space used: 323700 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: 53 (25.0 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