Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate BPHYT_RS15405 BPHYT_RS15405 aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__BFirm:BPHYT_RS15405 Length = 398 Score = 201 bits (512), Expect = 2e-56 Identities = 131/359 (36%), Positives = 195/359 (54%), Gaps = 18/359 (5%) Query: 29 DVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADF-NYD 87 D+I + IG+PDF P V AA A+ VT YT G LR+A+ + ADF D Sbjct: 39 DIIHMGIGEPDFTAPEPVIEAAASALRRGVTQYTSALGLHALREAISAHY---ADFYGVD 95 Query: 88 AE-SEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT-TSH 145 + + I++T GAS A+ A ++ DEV+MP P YP + +PV+V + + Sbjct: 96 VDPARIVVTAGASAALLLACAALVDRDDEVLMPDPCYPCNRHFVIAAEGRPVMVPSGPAE 155 Query: 146 GFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSE 205 F+LTA +E +T+ V+L PSNPTG ++ EL+ I ++ R F + DEIY Sbjct: 156 RFQLTAADVERLWNEHTRGVLLASPSNPTGTSIEPAELERIVKAVRARGGFTIVDEIYQG 215 Query: 206 LTYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCAS 265 L+YD S ++ D I +N SK +MTGWR+G+L P + K+ Q CAS Sbjct: 216 LSYDAKPVSALSF-GDDVITVNSFSKYFNMTGWRLGWLVVPPGMVSAFEKLAQNLFICAS 274 Query: 266 SISQKAAL---EAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLDV-VKPSGAFYIFPSI 321 +++Q AAL E T +A R+++K+R D++ L S+G V V P GAFY++ Sbjct: 275 ALAQHAALACFEPETIAIYEA--RRQEFKRRRDFIAPALESLGFSVPVMPDGAFYVYADC 332 Query: 322 KSFGMT----SFDFSMALLEDAGVALVPGSSFSTYG-EGYVRLSFACSMDTLREGLDRL 375 ++ + S + A+L DAGV LVPG F T+ + Y+RLS+A + L E +DRL Sbjct: 333 RTVAHSAAGDSAALTKAMLHDAGVVLVPGMDFGTHAPKDYIRLSYATAYPKLEEAVDRL 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: 343 Number of extensions: 16 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: 398 Length adjustment: 31 Effective length of query: 362 Effective length of database: 367 Effective search space: 132854 Effective search space used: 132854 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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