Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 202522 SO3415 aspartokinase I/homoserine dehydrogenase, threonine-sensitive (NCBI ptt file)
Query= BRENDA::P00561 (820 letters) >FitnessBrowser__MR1:202522 Length = 822 Score = 906 bits (2342), Expect = 0.0 Identities = 474/821 (57%), Positives = 590/821 (71%), Gaps = 10/821 (1%) Query: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60 M+V+KFGGTS+AN +RF ADI+ A VATVLSAPA +TN L+ M+ + G+D Sbjct: 1 MKVMKFGGTSLANWQRFSMAADIVAKAATMEPVATVLSAPATVTNALLEMVNLAVKGEDY 60 Query: 61 LPNISDAERIFAELL-----TGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCP 115 P I ER+F L +GL++ Q A L + A+ + LHGI+LL +CP Sbjct: 61 SPVIQHVERVFTSLYQDAVSSGLSSTQSELLFAGLGA----QLARWQDRLHGITLLQECP 116 Query: 116 DSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIA 175 D I A ++ GE++S A+M V+ A+G +DP + L G LES VDIA S R Sbjct: 117 DGICAEIVVAGERLSAALMEQVMLAKGITSAQLDPRKLFLGRGRPLESVVDIAVSKPRFK 176 Query: 176 ASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTC 235 + + +M GFTA +E G++V LGRNGSDYSAAVLAACL A CEIWTDVDGVY Sbjct: 177 NLLLDEKRVWVMPGFTAADEDGKVVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNT 236 Query: 236 DPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLI 295 DPR V DA+LL +SYQEAMELSYFGAKVLHP+TI PIAQF IPC IKN+ NP APGTL+ Sbjct: 237 DPRVVADAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPDAPGTLV 296 Query: 296 GASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSE 355 D L VK ISNL+N MF VSGPGMKGMVGMA+R AA+SR+ +SV LITQSS E Sbjct: 297 SNLADASGLQVKAISNLDNQTMFDVSGPGMKGMVGMASRTLAAISRSGVSVSLITQSSCE 356 Query: 356 YSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAK 415 YSISFCV S+ + + A+++EF LE+K LLEP+ + LAI+S++GDGMRT +G++A+ Sbjct: 357 YSISFCVATSESAKVKLALEQEFELEIKSDLLEPIEMRHDLAIVSLIGDGMRTHKGVAAR 416 Query: 416 FFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGG 475 FF ALA+A++NI+AIAQGSSERSIS V+ V HQ F+ Q ++VF++G G Sbjct: 417 FFQALAQASVNIIAIAQGSSERSISTVIEQRKTKHAVAACHQGFFDVQQYLDVFLVGCGN 476 Query: 476 VGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLG 535 VG LLEQ+K+Q LK +HI +RVCG+ NS +L + G++L NWQ LA +++ +L Sbjct: 477 VGAGLLEQIKQQAIVLKEQHISIRVCGIVNSSKMLLDSAGIDLNNWQNLLADSQQSSDLP 536 Query: 536 RLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYA 595 L+ VKE LLNPV+VDCTSS+ V++QY + + G HVVTPNKKANT YY LR Sbjct: 537 ALLAWVKEQQLLNPVLVDCTSSEQVSNQYLEVMNAGMHVVTPNKKANTRDYAYYQALRQT 596 Query: 596 AEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSE 655 A RR+FLY+TNVGAGLPVI+NL+ LL AGD+L KF+GILSGSLS+IFGKLDEGMS SE Sbjct: 597 ALTQRRQFLYETNVGAGLPVIDNLKKLLFAGDKLHKFNGILSGSLSFIFGKLDEGMSLSE 656 Query: 656 ATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDV 715 AT LARE +TEPDPRDDLSGMDVARK+LILARE G +LEL+DI ++ VLP F+ GDV Sbjct: 657 ATKLAREKCFTEPDPRDDLSGMDVARKVLILAREVGLKLELSDIVVDSVLPESFDDSGDV 716 Query: 716 AAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGE 775 +FMA L + D AARVA+A+ +GKVLRYVG I E+G C V+IAEVD DPL+ VK GE Sbjct: 717 ESFMARLPEADAAIAARVAEAKAQGKVLRYVGQI-EEGACHVRIAEVDATDPLYSVKGGE 775 Query: 776 NALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816 NALAFYS YYQP+P VLRGYGAG +VTAAG FAD+LRTL+W Sbjct: 776 NALAFYSRYYQPIPFVLRGYGAGTEVTAAGAFADVLRTLNW 816 Lambda K H 0.319 0.135 0.384 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: 1501 Number of extensions: 57 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: 820 Length of database: 822 Length adjustment: 42 Effective length of query: 778 Effective length of database: 780 Effective search space: 606840 Effective search space used: 606840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 56 (26.2 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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