Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate 6936718 Sama_0905 bifunctional aspartokinase I/homeserine dehydrogenase I (RefSeq)
Query= BRENDA::P00561 (820 letters) >FitnessBrowser__SB2B:6936718 Length = 821 Score = 886 bits (2290), Expect = 0.0 Identities = 464/820 (56%), Positives = 577/820 (70%), Gaps = 9/820 (1%) Query: 1 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA 60 M+V+KFGGTS+AN +RF A I+ A+ QVA VLSAPA +TN L+ M++ ++G D Sbjct: 1 MKVMKFGGTSLANWQRFDMAAAIVAEAAKASQVAAVLSAPATVTNGLLDMVDVAVTGGDY 60 Query: 61 LPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHV----LHGISLLGQCPD 116 + +F L Q + Q + + + KH L G++LLG+CPD Sbjct: 61 QAVLGRVVGVFEALFDDACQHQ----VPQCREHLFAALSAQKHAWQTRLEGVALLGECPD 116 Query: 117 SINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAA 176 + A ++ GE++S +M ++ A + +DP LA G LES VDI S R Sbjct: 117 GVRAEIVVAGERLSTELMVALMNAHWLSADKLDPRALFLAHGTPLESVVDIGVSKPRFKQ 176 Query: 177 SRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCD 236 + + + +M GFTA ++KG V LGRNGSDYSAAVLAACL A CEIWTDVDGVY D Sbjct: 177 LPLDSKRVWVMPGFTAADDKGRTVTLGRNGSDYSAAVLAACLDASSCEIWTDVDGVYNTD 236 Query: 237 PRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIG 296 PR V DA+LL +SYQEAMELSYFGAKVLHP+TI PIAQF IPC IKN+ NP+APGTL+ Sbjct: 237 PRVVADAKLLSQLSYQEAMELSYFGAKVLHPKTIAPIAQFHIPCYIKNSFNPEAPGTLVS 296 Query: 297 ASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEY 356 + DE L VK IS+L+N MF VSGPGMKGMVGMA+R A++RA +SV LITQSS EY Sbjct: 297 NAVDETGLQVKAISSLDNQTMFDVSGPGMKGMVGMASRTLGAIARAGVSVSLITQSSCEY 356 Query: 357 SISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKF 416 SISFCV D + + A+++EF LELK LLEPL + LAI+S++GDGMRT +G++AKF Sbjct: 357 SISFCVAGKDAAKVQSALEQEFELELKSELLEPLEMQSGLAIVSLIGDGMRTHKGVAAKF 416 Query: 417 FAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGV 476 F+ALA+A++NI AIAQGSSERSIS VV + HQ F+ Q ++VF++G G V Sbjct: 417 FSALAQASVNIRAIAQGSSERSISAVVEQRKVQNAIGACHQRFFDVQQYLDVFLVGAGNV 476 Query: 477 GGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGR 536 G LL Q+K Q LK +HI +RVCG+ANS+ +L + G++L NWQ L ++ +LG Sbjct: 477 GAGLLAQVKNQAEALKEQHISIRVCGIANSRKMLLDERGIDLANWQGLLNDSETGCDLGA 536 Query: 537 LIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAA 596 ++ KE LLNPV+VDCTSS AVAD+Y + + G HVVTPNKKANT + YY LR AA Sbjct: 537 MLAWAKEKQLLNPVLVDCTSSAAVADRYLEVMEAGMHVVTPNKKANTRDLGYYRALREAA 596 Query: 597 EKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEA 656 + RR+FLY+TNVGAGLPVI+NL+ LL AGD+L KF+GILSGSLS+IFGKL+EGMS SEA Sbjct: 597 LRHRRQFLYETNVGAGLPVIDNLKKLLCAGDKLHKFNGILSGSLSFIFGKLEEGMSLSEA 656 Query: 657 TTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVA 716 T++AR+ +TEPDPRDDLSGMDVARK+LILARE G LEL D+ ++ VLPA F+A GDV+ Sbjct: 657 TSIARDKCFTEPDPRDDLSGMDVARKVLILAREVGMPLELEDVVVDSVLPASFDANGDVS 716 Query: 717 AFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGEN 776 FMANL + D A V AR EGKVLRYVG IDE G CRV I V PLF VK GEN Sbjct: 717 TFMANLHKADTEIATMVENARSEGKVLRYVGQIDESG-CRVSIQAVGPEAPLFSVKGGEN 775 Query: 777 ALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSW 816 ALAFYS YYQP+P VLRGYGAG DVTAAG FADLLRTL+W Sbjct: 776 ALAFYSRYYQPIPFVLRGYGAGTDVTAAGAFADLLRTLNW 815 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: 1502 Number of extensions: 47 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: 820 Length of database: 821 Length adjustment: 42 Effective length of query: 778 Effective length of database: 779 Effective search space: 606062 Effective search space used: 606062 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