Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate H281DRAFT_04024 H281DRAFT_04024 Aspartate/methionine/tyrosine aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Burk376:H281DRAFT_04024 Length = 399 Score = 200 bits (508), Expect = 7e-56 Identities = 129/357 (36%), Positives = 191/357 (53%), Gaps = 14/357 (3%) Query: 29 DVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYDA 88 D+I + IG+PDF P V AA A+ VT YT G LR+A+ + + N D Sbjct: 39 DIIHMGIGEPDFTAPEPVIEAAANALRRGVTQYTSALGLHALREAISAHYAEVYGVNVDP 98 Query: 89 ESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT-TSHGF 147 + I++T GAS A+ A ++ DEV+MP P YP + KPV+V + + F Sbjct: 99 -ARIVVTAGASAALLLACAALVDRDDEVLMPDPCYPCNRHFVIAAEGKPVMVPSGPAERF 157 Query: 148 KLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSELT 207 +LTA +E T+ V+L PSNPTG ++ EL+ I ++ R F + DEIY L+ Sbjct: 158 QLTAADVERLWNERTRGVLLASPSNPTGTSIEPAELERIVKAVRARGGFTIVDEIYQGLS 217 Query: 208 YDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCASSI 267 YD S +Y D I +N SK +MTGWR+G+L P + K+ Q CAS++ Sbjct: 218 YDAKPVSALSY-GDDVITVNSFSKYFNMTGWRLGWLVVPPGMVSAFEKLAQNLFICASAL 276 Query: 268 SQKAAL---EAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDV-VKPSGAFYIFPSIKS 323 +Q AAL E T +A R ++K+R D++ L S+G V V P GAFY++ +S Sbjct: 277 AQHAALACFEPQTIATYEA--RRLEFKRRRDFIAPALESLGFTVPVMPDGAFYVYADCRS 334 Query: 324 FGM----TSFDFSMALLEDAGVALVPGSSFSTYG-EGYVRLSFACSMDTLREGLDRL 375 S + A+L +AGV LVPG F ++ + Y+RLS+A + + L E ++RL Sbjct: 335 VAHPAAGDSSALTKAMLHEAGVVLVPGMDFGSHAPKQYIRLSYATAYEKLEEAVERL 391 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: 337 Number of extensions: 19 Number of successful extensions: 8 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: 399 Length adjustment: 31 Effective length of query: 362 Effective length of database: 368 Effective search space: 133216 Effective search space used: 133216 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