Align fused aspartate kinase/homoserine dehydrogenase 1 (EC 2.7.2.4; EC 1.1.1.3) (characterized)
to candidate 7023422 Shewana3_0652 aspartate kinase III (RefSeq)
Query= ecocyc::ASPKINIHOMOSERDEHYDROGI-MONOMER (820 letters) >FitnessBrowser__ANA3:7023422 Length = 451 Score = 191 bits (484), Expect = 1e-52 Identities = 140/460 (30%), Positives = 226/460 (49%), Gaps = 18/460 (3%) Query: 3 VLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALP 62 V KFGGTSVA+ R ADI+ N V V+SA + +TN LV + +++++ L Sbjct: 5 VAKFGGTSVADYGAMNRCADIVLGNPDCRLV--VVSASSGVTNLLVELTQESMNDDGRLQ 62 Query: 63 NISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAAL 122 + +I +L L +P A L + + + +L Q + L Sbjct: 63 RLKQIAQIQYAILDKLG--RPNDVAAALDKLLS------RMAVLSEALASQRSKATMDEL 114 Query: 123 ICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIP-- 180 + GE+ S A+ A VL +G N + D L H+ + + + +P Sbjct: 115 LSLGEQCSSALFAAVLREKGANSSAFDVRRVLRTDSHFGRAEPQVEQIAILSREHLLPLL 174 Query: 181 ADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQV 240 ++ +++ GF +E G+ LGR GSDYSAA+LA L+A EIWTDV G+YT DPR Sbjct: 175 SEQVIVTQGFIGSDEAGQTTTLGRGGSDYSAALLAEALKASAVEIWTDVAGIYTTDPRLA 234 Query: 241 PDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRD 300 P+A + +S+ EA E++ FGAKVLHP TI P + QI + ++ P+ GT I + Sbjct: 235 PNAHPIAEISFNEAAEMATFGAKVLHPATILPAVRQQIQVFVGSSKEPEKGGTWI-RHQV 293 Query: 301 EDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISF 360 ED + ++ + + ++ M G A FA ++R +ISV LIT S S++ Sbjct: 294 EDAPVFRAVALRRDQTLLNLHSLQMLHAQGFLAETFATLARHKISVDLITTSEVNVSLTL 353 Query: 361 CVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAAL 420 SD + + E EL + + V + LA+++++G+ + T GI + F L Sbjct: 354 DKTGSDS-SGQGLLSEALLQELSQHC--RVRVEDGLALVAIIGNRIATTAGICRRVFEVL 410 Query: 421 ARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLF 460 N+ + I QG+S ++ V+V +A V+ H+ LF Sbjct: 411 EPHNVRM--ICQGASPHNLCVLVAESEAAQVVKALHENLF 448 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: 661 Number of extensions: 23 Number of successful extensions: 4 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: 451 Length adjustment: 37 Effective length of query: 783 Effective length of database: 414 Effective search space: 324162 Effective search space used: 324162 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: 53 (25.0 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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