Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate PfGW456L13_2943 Aspartate aminotransferase (EC 2.6.1.1)
Query= curated2:B1I544 (392 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2943 Length = 395 Score = 181 bits (460), Expect = 2e-50 Identities = 122/362 (33%), Positives = 177/362 (48%), Gaps = 5/362 (1%) Query: 28 KAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPSSAGMPAYRRAVADWYARRF 87 + QGVDV+ L IGDPD TP I++AA L H YP+ G R ++A + RR Sbjct: 28 REQGVDVLLLSIGDPDFDTPQPIVQAAIGSLLAGDTH-YPAVRGSQGLRDSIARHHRRRS 86 Query: 88 GVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILAGGIPHPVPL 147 G +D Q +V G++ + + C +DPGD VLV +P Y Y G G PVP+ Sbjct: 87 GQAVDAQHVIV-FPGAQCAVYSVAQCLLDPGDEVLVAEPMYVTYEGVFGACGAKVVPVPV 145 Query: 148 TAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKEFFARVVDFAREYGILVCHDA 207 + NGF D A + A + M +N PNNP+GA + + + + + D Sbjct: 146 RSQNGFRVDPADVAALITPNTRAMLLNSPNNPSGASLPLTAWKALAALCIRHDLWLISDE 205 Query: 208 AYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTGWRAGWAAGNAGAVEALGRLKS 267 YSE+ F+G S + G E +S+SK++ M+GWR GW G E L L Sbjct: 206 VYSELLFEG-EHISPASLPGMAERTATINSLSKSHAMSGWRVGWVIGPQSLCEHLVNLSL 264 Query: 268 NLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDL-GWRLTRPRATFYI 326 + G+ +Q AA AL+ V + E YR+RRDLV +LN G + RP ++ Sbjct: 265 CMLFGIPDFIQNAAQLALDENLPHVAQMREEYRQRRDLVCASLNLCPGIQAIRPDGGMFV 324 Query: 327 WAPV-PAGHDASSFAEMVLEKAGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERLRG 385 V G A FAE +L+ GV + G +G G+ RI L + P+L +A R+ Sbjct: 325 MVDVRQTGLSAQHFAERLLDGYGVSVLAGEAFGPSAAGHIRIGLVVDRPKLADACRRIVM 384 Query: 386 CL 387 C+ Sbjct: 385 CV 386 Lambda K H 0.321 0.139 0.430 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: 310 Number of extensions: 16 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: 392 Length of database: 395 Length adjustment: 31 Effective length of query: 361 Effective length of database: 364 Effective search space: 131404 Effective search space used: 131404 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: 50 (23.9 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