Align aspartate kinase / homoserine dehydrogenase (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate WP_062058105.1 N456_RS13555 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Cola:Echvi_2000 (815 letters) >NCBI__GCF_001401755.1:WP_062058105.1 Length = 814 Score = 736 bits (1901), Expect = 0.0 Identities = 375/814 (46%), Positives = 564/814 (69%), Gaps = 5/814 (0%) Query: 1 MKIIKFGGSSIANYENIQKVFSIIEQKSEKEAFALVFSAFGGVTEQLLQCANIAQQSEES 60 M ++KFGGSS+AN I+ V II+Q+S+K+ +V SA GG+T+ LLQ A + E+ Sbjct: 1 MNVLKFGGSSVANATTIENVIQIIKQQSKKQPLYVVVSAMGGITDLLLQAGEEASANNEN 60 Query: 61 YHTILQELEKRHLEIVKKLVPVQQQSTALTFVKVRFNELGDLFHGIYLIKECSNRTMDYV 120 Y L E+EKRHL+ VK L+P+ QS ++ VK + N L L G+YL+KE S +T + Sbjct: 61 YKNTLVEIEKRHLDAVKALIPIVSQSAIISKVKAQLNILESLCEGVYLLKELSVKTTAVI 120 Query: 121 LSFGERLSNFILAAGLQAKGIGTSYVDARDLV-KTDDRFGHAKVNFKTTNKLIQDHFKSH 179 SFGE LS++I+ + K + + D+RD++ KT + +++ TN I++ ++ Sbjct: 121 SSFGELLSSYIITEAAKIKELDITLKDSRDIIIKTTN--SKVTIDYNETNHRIKELKNTN 178 Query: 180 DD-IKVITGFIGSTEKGETTTVGRSGSDYTASIFAAALGAEQVEIWTDVSGVMTADPRLV 238 I + GFI ST+ GE TT+GR GSD+TA+I AA++ A +++IWTDVSG+ TA P+LV Sbjct: 179 THRICLFPGFIASTQDGEPTTLGRGGSDFTAAILAASINANELQIWTDVSGMYTAHPKLV 238 Query: 239 YTAFTIPQLSYNEAMELSHFGAKVVFPATMQPAMKEDIPIYIKNTFKPDEAGTRIS-KDS 297 A + +SY EAMELSHFGAKV++P T+ P +++DIPI IKNTFKP + GT I+ K Sbjct: 239 KQAKPVHHISYQEAMELSHFGAKVIYPPTIHPVLEKDIPIVIKNTFKPLDKGTLITRKVD 298 Query: 298 GEGKIIKGISSMDNISILNVQGPGLVEVVGVSQRFFGTLANNGINIILISQASSEHSICV 357 K + GIS +D+I++++++G G+V + G S+R F L INIILI+QASSEHSIC+ Sbjct: 299 DRKKAVTGISHIDSITVISLEGSGMVGIPGFSKRLFEALFLENINIILITQASSEHSICL 358 Query: 358 AIASKDASRAKSVIEEEFRYEIQSGEMDEIQIVPDMAVIAVVGENMQHNPGASGRMFQAL 417 A+ + +A +AK++++ F +EI ++D ++I +A++A+VG+NM H+ G SG+MF L Sbjct: 359 AVNTNEAEKAKNILDVAFEFEISKHKLDPVKIENGVAIVALVGDNMYHHQGLSGKMFSTL 418 Query: 418 GRNNVNVAAIAQGSSELNISAVITQADLQKALNALHEAFFLSDYKVLHLFLVGVGLIGKA 477 G+NNVN+ AIAQG+SE NIS VI + D++KALN LHE FF K L+LF+ GVG +G Sbjct: 419 GKNNVNIRAIAQGASEKNISVVIAKKDIKKALNILHEEFFEVKTKQLNLFITGVGNVGGK 478 Query: 478 LTKMIHQQLKNLQEENMLDIQIHGMANSRYMKFHEDGFDLATVGPPDENDEPMDMDKFIG 537 L + + QQ K L+++ L I+I G++NSR M F E G DL + E + + F Sbjct: 479 LIEQLKQQNKYLKDKLRLKIRITGISNSRMMVFDETGIDLDSWQEVLSKGEKANAELFFT 538 Query: 538 TMTEMNFSNSVFVDCTASQDVADIYEQILDSKVGIVTPNKKANSGPLETYKKLKKLAGQR 597 + EMN NS+FVD TA+ D+A IY+ L + +VT NK A + Y++L+ L+ + Sbjct: 539 KVKEMNLRNSIFVDNTANPDIAKIYKHYLAESMAVVTCNKIACADDYNNYQELQDLSRKF 598 Query: 598 GVRFFYETNVAAGLPVINTLQDLMLSGDHVHRIEAVLSGSMNYIFSELEKGMPFSEVVAQ 657 F YETNV AGLP+I+TL +L+ SGD+VH+I+AVLSGS+N++F+ +G+ F ++V Q Sbjct: 599 NASFLYETNVGAGLPIIDTLNNLIASGDNVHKIQAVLSGSLNFVFNNYIEGVTFHDIVKQ 658 Query: 658 AKEKGYTEPDPRDDLSGMDVARKILILGREAGQDLHFEDVEIQSMVPEDCEDAASVPEFF 717 A+++GYTEPDP+ DLSG+DVARKILIL RE+G + ED+E + +P++ ++++V +F Sbjct: 659 AQQQGYTEPDPKIDLSGVDVARKILILARESGNIMELEDIENDAFLPKESVESSTVNDFL 718 Query: 718 KKLQKHDGHFQQLLDEANAKGEKLRFMATLENGKAKVGLNSLDSEHPFFTLKGSDNMILF 777 + L++++ HF+++L EAN K +L+++A E+GKAKVGL + +HPF+ L+GSDN++LF Sbjct: 719 ESLKENEAHFKKILTEANTKECRLKYVAQYESGKAKVGLQHIPKDHPFYNLEGSDNIVLF 778 Query: 778 TTERYNDFPMIVRGPGAGADVTAAGVFADIIRLG 811 T+RY P+I++G GAGA+VTA+G+FADIIR+G Sbjct: 779 YTDRYPKQPLIIKGAGAGAEVTASGIFADIIRIG 812 Lambda K H 0.317 0.134 0.375 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: 1459 Number of extensions: 63 Number of successful extensions: 5 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: 815 Length of database: 814 Length adjustment: 41 Effective length of query: 774 Effective length of database: 773 Effective search space: 598302 Effective search space used: 598302 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)
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