Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_073036823.1 BUB04_RS02820 aspartate--tRNA ligase
Query= reanno::Miya:8501305 (614 letters) >NCBI__GCF_900129305.1:WP_073036823.1 Length = 595 Score = 751 bits (1938), Expect = 0.0 Identities = 360/594 (60%), Positives = 460/594 (77%), Gaps = 4/594 (0%) Query: 16 IEPLGDWVRSHDCATLTAADTGAEVCLMGWVQYRRDHGGLIFVDLRDRQGLTQIVFSPDV 75 ++PLG+W ++HDC TL G +V LMGWVQ RRDHGGLIFVDLRDR+G+TQ+VF P Sbjct: 2 LDPLGEWKKTHDCNTLGLGHAGEQVVLMGWVQRRRDHGGLIFVDLRDREGITQVVFDPQA 61 Query: 76 NPAAHERAHIIRSEYVLAIRGTVRPRPEGMTNPGMKTGEIEVYVSEWKLLNTSKTPAFVI 135 + AHERAH +RSE+V+A+RGTVR RPEGMTNP +KTGEIEV V + K+LN +KTP F I Sbjct: 62 DALAHERAHGLRSEFVIAVRGTVRRRPEGMTNPKLKTGEIEVLVHDLKILNVAKTPPFHI 121 Query: 136 EDRTEASENLRLQYRYLDLRRPRMANNFIVRHKAAQATRRYLDELGFLEIETPYLTKSTP 195 ED TEASE++RL+YRYLDLRRP M N I+RH+AA TR Y + GF+E+ETP LTKSTP Sbjct: 122 EDDTEASESIRLKYRYLDLRRPVMQRNLILRHRAAFLTRNYFADHGFVEVETPVLTKSTP 181 Query: 196 EGARDFLVPSRLNQGQFYALPQSPQLFKQLLMMSGMERYYQIVRCFRDEDMRADRQLEFT 255 EGARD+LVPSR+N G+FYALPQSPQ+FKQLLM++G ERY QIV+CFRDED+RADRQ EFT Sbjct: 182 EGARDYLVPSRVNPGKFYALPQSPQIFKQLLMVAGFERYMQIVKCFRDEDLRADRQPEFT 241 Query: 256 QIDIEMSFVDEEQVMAMAEGLMARVFRDALDREIATPFPRMSYDDAMARYGVDKPDTRFG 315 Q+D+EMSF+ EE V A+ EG + R+F++ L E++TPFPRM+Y DAM RYG D+PDTRFG Sbjct: 242 QLDLEMSFIHEEDVFALIEGWICRLFQELLGVELSTPFPRMTYADAMNRYGTDRPDTRFG 301 Query: 316 LELQDVTHIVRGSNFKLFATA----ELVKAMRVPGGETMTRKEIDEFTEFVKIYGAQGLA 371 LEL D+T IV+ +F++F A VK++ +PGG ++RK++D+ EFV+ +GA+G+A Sbjct: 302 LELVDLTEIVKDCDFRVFRQAVESGGRVKSICLPGGSRLSRKDLDDLIEFVQGFGAKGMA 361 Query: 372 WIKIRPDEWQSPIAKFLSDEERAGLKDALGLETGDIVFFQAGAPGMVNAALGNLRVRLGE 431 WIK++PD WQSPI KFLS+ R + +A G GDI+FF A P +V+ +LGNLR RL Sbjct: 362 WIKVQPDGWQSPITKFLSEGVRGAIAEATGAGQGDILFFVADQPKVVHESLGNLRNRLAR 421 Query: 432 HLGLIDENAFNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHMDVMVENPAAARARAY 491 + L+++ AF F WVT FPL E+D +EKRYVA HHPFT+P + + ++ E P R+RAY Sbjct: 422 QMNLVEDGAFQFCWVTHFPLLEWDPDEKRYVAVHHPFTAPLEEDLPLLDEAPEKVRSRAY 481 Query: 492 DMVLNGYELGGGSIRNHTAEKQRRMFAALGFSPEEAEAQFGFLTQALEMGAPPHGGIAFG 551 D+VLNG E+GGGSIR H + Q +MFAALG PEEA +FGFL AL+ GAPPHGGIAFG Sbjct: 482 DLVLNGTEIGGGSIRIHRQDIQNKMFAALGIGPEEAAEKFGFLLDALQFGAPPHGGIAFG 541 Query: 552 MDRLAMLLTGSSSIRDVIAFPKTQKATCLLTQAPDSVSARQLRDLGLRLRETGK 605 DRL ML++G++SIRDVIAFPKTQKATCL++ AP QL +L +R+ G+ Sbjct: 542 FDRLLMLMSGAASIRDVIAFPKTQKATCLMSGAPSEADINQLLELCIRVETEGR 595 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: 1053 Number of extensions: 36 Number of successful extensions: 2 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: 595 Length adjustment: 37 Effective length of query: 577 Effective length of database: 558 Effective search space: 321966 Effective search space used: 321966 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 10 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