Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate BWI76_RS10245 BWI76_RS10245 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Koxy:BWI76_RS10245 Length = 402 Score = 181 bits (458), Expect = 4e-50 Identities = 129/374 (34%), Positives = 194/374 (51%), Gaps = 28/374 (7%) Query: 23 LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82 L A + VI+L G+ DF TP H+ A +AI + T YT +G L+ A+ + Sbjct: 28 LEAAGKQVINLGEGELDFATPPHISYAGIEAIVHHQTKYTAVSGTAALKTAIAAKFARDN 87 Query: 83 DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142 Y E EII +GA Q I AF L G +VI+P P + Y +++L +PVIV Sbjct: 88 QLRYRPE-EIIAGSGAKQLIFNAFLATLDAGQQVIIPAPYWVSYPDMVSLADGEPVIVPC 146 Query: 143 TS-HGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGR-NVFVLSD 200 HG+KLT + ALTP+T+ ++L P NPTG SE EL+++A +L +V V++D Sbjct: 147 DEQHGWKLTPEQLAAALTPSTRWLILNSPGNPTGAIYSEPELRALADVLADYPHVLVMAD 206 Query: 201 EIYSELTYDRPHY----SIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKV 256 +IY L YD + A L +T+ +NG+SKSH+MTGWR+G+ P+ + + + Sbjct: 207 DIYEPLRYDNVPFITFAQAAPQLVSRTLTVNGVSKSHAMTGWRLGYAGGPQWLIAAMQIL 266 Query: 257 HQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-----GLDVVKP 311 + S SSISQ AA+ A+ + D + + RLD +++ M GL P Sbjct: 267 QSQSTSNPSSISQAAAIAALNHSAD----FFDGWLHRLDKRRQQVLGMIAATEGLSAGIP 322 Query: 312 SGAFYIFPSIKSF-------GMTSFDFSMA---LLEDAGVALVPGSSFSTYGEGYVRLSF 361 GAFY+F + + G T D S LLE VA++ GS+F GY+R+++ Sbjct: 323 QGAFYVFANCQQLIGRVTPGGETLRDDSGLANWLLEHTQVAVLHGSAFGM--PGYLRIAY 380 Query: 362 ACSMDTLREGLDRL 375 A L + R+ Sbjct: 381 AVEDGLLAQACQRI 394 Lambda K H 0.319 0.135 0.388 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: 341 Number of extensions: 20 Number of successful extensions: 6 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: 393 Length of database: 402 Length adjustment: 31 Effective length of query: 362 Effective length of database: 371 Effective search space: 134302 Effective search space used: 134302 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