Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate SMc01578 SMc01578 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Smeli:SMc01578 Length = 400 Score = 223 bits (569), Expect = 6e-63 Identities = 144/378 (38%), Positives = 213/378 (56%), Gaps = 20/378 (5%) Query: 18 RKFSNLVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLY 77 +K L A+ DVI L G+PDF TP ++K AA AID T YTP +G ELR+A+ Sbjct: 21 QKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPELREAIAKK 80 Query: 78 MKKKADFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKP 137 K++ + +Y A ++ I+ TG Q + AF L+PGDEV++P P + Y ++ LCG P Sbjct: 81 FKRENNLDYTA-AQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALCGGTP 139 Query: 138 VIVDT-TSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIA-ALLKGRNV 195 V V T + FKL A ++ A+TP TK V PSNP+G S EELK++ L+K +V Sbjct: 140 VFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMKHPHV 199 Query: 196 FVLSDEIYSELTYDRPHYS----IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAK 251 +VL+D++Y LTY ++ + L ++T+ +NG+SK+++MTGWRIG+ P + K Sbjct: 200 WVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAGPLHLIK 259 Query: 252 HILKVHQYNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRL-VSMGLDVVK 310 + + S A+SI+Q AA+EA+ D +E ++ R D V L + G+ Sbjct: 260 AMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAKGISCPT 319 Query: 311 PSGAFYIFPSIKS-FGMTS---------FDFSMALLEDAGVALVPGSSFSTYGEGYVRLS 360 P GAFY++PS G T+ DF LLE GVA+V GS+F G + R+S Sbjct: 320 PEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAFG-LGPNF-RIS 377 Query: 361 FACSMDTLREGLDRLELF 378 +A S L E R++ F Sbjct: 378 YATSEALLEEACRRIQRF 395 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: 354 Number of extensions: 21 Number of successful extensions: 7 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: 400 Length adjustment: 31 Effective length of query: 362 Effective length of database: 369 Effective search space: 133578 Effective search space used: 133578 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 Jul 25 2024. The underlying query database was built on Jul 25 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