Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate CA265_RS07515 CA265_RS07515 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Pedo557:CA265_RS07515 Length = 380 Score = 250 bits (639), Expect = 4e-71 Identities = 145/369 (39%), Positives = 218/369 (59%), Gaps = 18/369 (4%) Query: 23 LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82 L ++ ++ISL++G+PDF TP HVK AAKKA+DEN T Y+P GY +LRQA+ +K + Sbjct: 8 LASKGINIISLSVGEPDFNTPDHVKNAAKKALDENYTRYSPVPGYPDLRQAIVNKLKTEN 67 Query: 83 DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142 + +YD S+I+++TGA Q++ T++ P DEVI+P P + Y ++ L K V +DT Sbjct: 68 NLDYDI-SQIVVSTGAKQSLSNVILTLIDPDDEVIIPTPYWVSYSEMVTLAEGKSVFIDT 126 Query: 143 -TSHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALL-KGRNVFVLSD 200 FK+T +E A+TP +K + P NPTG S+EEL ++ A+ K N+++LSD Sbjct: 127 DIESDFKITPAQLEAAITPKSKLFMFSSPCNPTGSVYSKEELAALVAVFEKHPNIYILSD 186 Query: 201 EIYSELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQ 258 EIY + + H SIA + ++D+ I++NG SK+ +MTGWR+G++ A K+IA K+ Sbjct: 187 EIYEHINFVDKHESIAQFDSIKDRVIIVNGFSKAFAMTGWRLGYIAANKEIAAANDKLQG 246 Query: 259 YNVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYI 317 S SI+Q+A + A G L M+E + +R + VY+ L + G+ P GAFY Sbjct: 247 QTTSGTCSIAQRAGIVAYEQGLASVLEMKEAFLRRRELVYNLLNEIPGVKTNLPDGAFYF 306 Query: 318 FPSIKSFG----------MTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDT 367 FP I SF S D ++ LL VA V G SF Y+RLS+A S ++ Sbjct: 307 FPEISSFFGKKDADGNVIKDSSDLALYLLNVGHVATVGGDSFG--NNNYIRLSYAASDES 364 Query: 368 LREGLDRLE 376 L E L R++ Sbjct: 365 LVEALRRIK 373 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: 346 Number of extensions: 17 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: 380 Length adjustment: 30 Effective length of query: 363 Effective length of database: 350 Effective search space: 127050 Effective search space used: 127050 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