Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate Pf1N1B4_4996 Aspartate aminotransferase (EC 2.6.1.1)
Query= curated2:B1I544 (392 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4996 Length = 395 Score = 174 bits (442), Expect = 3e-48 Identities = 122/374 (32%), Positives = 180/374 (48%), Gaps = 5/374 (1%) Query: 19 RIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPSSAGMPAYRRA 78 +I + + QGVDV+ L IGDPD TP II AA L H Y G R + Sbjct: 19 KIHDRALELREQGVDVLLLSIGDPDFDTPLPIIHAAIDSLLAGDTH-YSDVRGTRTLRSS 77 Query: 79 VADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILA 138 +A + RR G +D +V L G++ + + C +DPGD V+V +P Y Y G Sbjct: 78 IASRHQRRSGQLVDADHVIV-LPGAQCAVYSVAQCLLDPGDEVIVAEPMYVTYEGVFGAC 136 Query: 139 GGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKEFFARVVDFARE 198 G PV + NGF + A + A + +V+ +N PNNP+GA S + + + + Sbjct: 137 GASVVPVAVRPENGFRVEPADVAALITSKTRVILLNSPNNPSGASLSLKSWKALAALCVQ 196 Query: 199 YGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTGWRAGWAAGNAGA 258 + + + D YS++ F+G S + G E +S+SK++ MTGWR GW G Sbjct: 197 HDLWLISDEVYSDLLFEG-EHISPASLPGMAERTATINSLSKSHAMTGWRVGWMIGPKPL 255 Query: 259 VEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDL-GWRL 317 E L L + G+ VQ AA AL+ V + E YR+RRDLV L+ G R Sbjct: 256 AEHLMHLSLCMLFGLPDFVQNAAQVALDKDLPEVALMREEYRQRRDLVCARLSGCPGIRP 315 Query: 318 TRPRATFYIWAPV-PAGHDASSFAEMVLEKAGVVITPGTGYGTYGEGYFRISLTLPTPRL 376 +P ++ V G A FAE +LE GV + G +G G+ RI L + RL Sbjct: 316 IKPDGGMFVMVDVRQTGLGAQDFAERLLEGYGVSVLAGEAFGPSAAGHIRIGLVVDQARL 375 Query: 377 VEAMERLRGCLGRV 390 +A +R+ C ++ Sbjct: 376 ADACQRIASCAAQL 389 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: 291 Number of extensions: 14 Number of successful extensions: 3 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 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