Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate N515DRAFT_2186 N515DRAFT_2186 alanine-synthesizing transaminase
Query= BRENDA::Q56232 (385 letters) >FitnessBrowser__Dyella79:N515DRAFT_2186 Length = 410 Score = 167 bits (422), Expect = 6e-46 Identities = 119/384 (30%), Positives = 182/384 (47%), Gaps = 19/384 (4%) Query: 18 AVNAKALELRRQGVDLVALTAGEPD---FDTPEHVKEAARRALAQGKTKYAPPAGIPELR 74 A+ ++ EL G+ ++ L G P F+TP H+++A L + Y G+ E R Sbjct: 18 ALTRRSRELEAAGLPIIKLNIGNPGRYGFETPPHLRDAIAAHLRDSEA-YGHEQGLEEAR 76 Query: 75 EALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRF 134 E +A + R V E V G + + +A+L PGDEV++ SP + + Sbjct: 77 ETIAAQQRARGARGVEVERIFVGNGVSELIDLSLRALLQPGDEVLLPSPDYPLWSAATIL 136 Query: 135 AGGVVVEVETLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAV 194 G L E G +PDP+ + +T RT+A+V+ +PNNPTGAVYP+E+LE + R+A Sbjct: 137 NDGQPRYYRCLAENGHLPDPDEIEALVTARTRAIVLINPNNPTGAVYPRELLERIVRIAE 196 Query: 195 EHDFYLVSDEIYEHLLYEGEHFSP-GRVAPE-HTLTVNGAAKAFAMTGWRIGYACGPKEV 252 H L++DEIY+ +LY+G F P VA + ++ G +K G+R+G+ + Sbjct: 197 RHHLLLLTDEIYDEILYDGAQFVPLATVAGDVPCVSFGGLSKVHRACGYRVGWMSLSGDP 256 Query: 253 IKA-----MASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGL 307 ++ + + + AQWA AL ++ A + RR ++LEG+ Sbjct: 257 VRTHDYRDALQLLAALRLCANVTAQWAVRPALESKPTIGALTSPGGRLHEARR-MILEGV 315 Query: 308 -TALGLKAVRPSGAFY----VLMDTSPIAPDEVRAAERLLEAGVAVVPGTDFAA--FGHV 360 + L P GA Y V D P D A L E V VVPG+ F H+ Sbjct: 316 ANSEFLDLATPGGALYAFPRVRADRVPRFDDNAFALRLLEEESVLVVPGSSFNVPDSRHL 375 Query: 361 RLSYATSEENLRKALERFARVLGR 384 RL+ E LR+ R RVL R Sbjct: 376 RLTLLPPPEQLREVFVRIERVLAR 399 Lambda K H 0.317 0.133 0.379 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: 422 Number of extensions: 22 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: 385 Length of database: 410 Length adjustment: 31 Effective length of query: 354 Effective length of database: 379 Effective search space: 134166 Effective search space used: 134166 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: 50 (23.9 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