Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (characterized)
to candidate AO353_26890 AO353_26890 aspartate aminotransferase
Query= SwissProt::Q2RK33 (390 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26890 Length = 395 Score = 162 bits (409), Expect = 2e-44 Identities = 114/370 (30%), Positives = 176/370 (47%), Gaps = 11/370 (2%) Query: 17 RIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPENHRYPTSEGLLAFRQA 76 +I + E RE+GVD++ L +GDPD TP ++ + + H Y G + R + Sbjct: 19 QIHYRALELREQGVDVLLLSVGDPDFDTPKPIVQAAIDSLLAGDTH-YSEVRGTRSLRTS 77 Query: 77 VADWYQRLYG--VDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLVPDPGYPVYNIGTL 134 +A + R G VD D V+ L G++ + + C +DPGD LV +P Y Y Sbjct: 78 IARRHTRRSGQVVDAD---HVLVLPGAQCAVYSVVQCLLDPGDEVLVAEPMYVTYEGVFG 134 Query: 135 LAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAVADLKFFQEVVEFA 194 G + + + NGF D I + + R + + +N PNNP+GA L +Q + Sbjct: 135 ACGAKVVPIAVRPENGFRVDPTDIAARITPRTRAILLNSPNNPSGASLSLAIWQALARLC 194 Query: 195 RSYDLIVCHDAAYSEITYDG-YRAPSFLQAPGAKEVGIEFNSVSKPYNMTGWRLGWACGR 253 +DL + D YSE+ Y+G + +P+ L PG E NS+SK + MTGWR+GW G Sbjct: 195 VKHDLWLISDEVYSELLYEGEHISPASL--PGMAERTATVNSLSKSHAMTGWRVGWVIGP 252 Query: 254 ADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERRDIIVEGFNSL-G 312 + E L + + G VQ A AL LA +R Y+ RRD++ G Sbjct: 253 KRLTEHLENLSLCMLFGIPDFVQNAARVALEADLPELALMRNEYRARRDLVCARLGDCPG 312 Query: 313 WHLEKPKATFYVWAPVPR-GYTSASFAEMVLEKAGVIITPGNGYGNYGEGYFRIALTISK 371 P +V V + G + +FAE +LE V + G +G G+ RI L + + Sbjct: 313 ISPVIPDGGMFVMVDVRQTGVGAQAFAEKLLEGYAVSVLAGEAFGPSAAGHIRIGLVLDQ 372 Query: 372 ERMQEAIERL 381 +R+ EA R+ Sbjct: 373 QRLAEACRRI 382 Lambda K H 0.320 0.139 0.421 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: 372 Number of extensions: 21 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: 390 Length of database: 395 Length adjustment: 31 Effective length of query: 359 Effective length of database: 364 Effective search space: 130676 Effective search space used: 130676 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