Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate 8501305 DvMF_2038 aspartyl-tRNA synthetase (RefSeq)
Query= reanno::Miya:8501305 (614 letters) >FitnessBrowser__Miya:8501305 Length = 614 Score = 1236 bits (3199), Expect = 0.0 Identities = 614/614 (100%), Positives = 614/614 (100%) Query: 1 MSDQKLDVQQEHQQYIEPLGDWVRSHDCATLTAADTGAEVCLMGWVQYRRDHGGLIFVDL 60 MSDQKLDVQQEHQQYIEPLGDWVRSHDCATLTAADTGAEVCLMGWVQYRRDHGGLIFVDL Sbjct: 1 MSDQKLDVQQEHQQYIEPLGDWVRSHDCATLTAADTGAEVCLMGWVQYRRDHGGLIFVDL 60 Query: 61 RDRQGLTQIVFSPDVNPAAHERAHIIRSEYVLAIRGTVRPRPEGMTNPGMKTGEIEVYVS 120 RDRQGLTQIVFSPDVNPAAHERAHIIRSEYVLAIRGTVRPRPEGMTNPGMKTGEIEVYVS Sbjct: 61 RDRQGLTQIVFSPDVNPAAHERAHIIRSEYVLAIRGTVRPRPEGMTNPGMKTGEIEVYVS 120 Query: 121 EWKLLNTSKTPAFVIEDRTEASENLRLQYRYLDLRRPRMANNFIVRHKAAQATRRYLDEL 180 EWKLLNTSKTPAFVIEDRTEASENLRLQYRYLDLRRPRMANNFIVRHKAAQATRRYLDEL Sbjct: 121 EWKLLNTSKTPAFVIEDRTEASENLRLQYRYLDLRRPRMANNFIVRHKAAQATRRYLDEL 180 Query: 181 GFLEIETPYLTKSTPEGARDFLVPSRLNQGQFYALPQSPQLFKQLLMMSGMERYYQIVRC 240 GFLEIETPYLTKSTPEGARDFLVPSRLNQGQFYALPQSPQLFKQLLMMSGMERYYQIVRC Sbjct: 181 GFLEIETPYLTKSTPEGARDFLVPSRLNQGQFYALPQSPQLFKQLLMMSGMERYYQIVRC 240 Query: 241 FRDEDMRADRQLEFTQIDIEMSFVDEEQVMAMAEGLMARVFRDALDREIATPFPRMSYDD 300 FRDEDMRADRQLEFTQIDIEMSFVDEEQVMAMAEGLMARVFRDALDREIATPFPRMSYDD Sbjct: 241 FRDEDMRADRQLEFTQIDIEMSFVDEEQVMAMAEGLMARVFRDALDREIATPFPRMSYDD 300 Query: 301 AMARYGVDKPDTRFGLELQDVTHIVRGSNFKLFATAELVKAMRVPGGETMTRKEIDEFTE 360 AMARYGVDKPDTRFGLELQDVTHIVRGSNFKLFATAELVKAMRVPGGETMTRKEIDEFTE Sbjct: 301 AMARYGVDKPDTRFGLELQDVTHIVRGSNFKLFATAELVKAMRVPGGETMTRKEIDEFTE 360 Query: 361 FVKIYGAQGLAWIKIRPDEWQSPIAKFLSDEERAGLKDALGLETGDIVFFQAGAPGMVNA 420 FVKIYGAQGLAWIKIRPDEWQSPIAKFLSDEERAGLKDALGLETGDIVFFQAGAPGMVNA Sbjct: 361 FVKIYGAQGLAWIKIRPDEWQSPIAKFLSDEERAGLKDALGLETGDIVFFQAGAPGMVNA 420 Query: 421 ALGNLRVRLGEHLGLIDENAFNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHMDVMV 480 ALGNLRVRLGEHLGLIDENAFNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHMDVMV Sbjct: 421 ALGNLRVRLGEHLGLIDENAFNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHMDVMV 480 Query: 481 ENPAAARARAYDMVLNGYELGGGSIRNHTAEKQRRMFAALGFSPEEAEAQFGFLTQALEM 540 ENPAAARARAYDMVLNGYELGGGSIRNHTAEKQRRMFAALGFSPEEAEAQFGFLTQALEM Sbjct: 481 ENPAAARARAYDMVLNGYELGGGSIRNHTAEKQRRMFAALGFSPEEAEAQFGFLTQALEM 540 Query: 541 GAPPHGGIAFGMDRLAMLLTGSSSIRDVIAFPKTQKATCLLTQAPDSVSARQLRDLGLRL 600 GAPPHGGIAFGMDRLAMLLTGSSSIRDVIAFPKTQKATCLLTQAPDSVSARQLRDLGLRL Sbjct: 541 GAPPHGGIAFGMDRLAMLLTGSSSIRDVIAFPKTQKATCLLTQAPDSVSARQLRDLGLRL 600 Query: 601 RETGKDGAPNAPQG 614 RETGKDGAPNAPQG Sbjct: 601 RETGKDGAPNAPQG 614 Lambda K H 0.321 0.137 0.407 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: 1428 Number of extensions: 42 Number of successful extensions: 1 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: 614 Length of database: 614 Length adjustment: 37 Effective length of query: 577 Effective length of database: 577 Effective search space: 332929 Effective search space used: 332929 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 (21.9 bits) S2: 53 (25.0 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