Align aspartyl-tRNA(Asp/Asn) synthetase (EC 6.1.1.23) (characterized)
to candidate WP_013705561.1 DESAC_RS02785 aspartate--tRNA ligase
Query= reanno::Miya:8501305 (614 letters) >NCBI__GCF_000195295.1:WP_013705561.1 Length = 593 Score = 714 bits (1842), Expect = 0.0 Identities = 350/590 (59%), Positives = 442/590 (74%), Gaps = 5/590 (0%) Query: 16 IEPLGDWVRSHDCATLTAADTGAEVCLMGWVQYRRDHGGLIFVDLRDRQGLTQIVFSPDV 75 ++ L R+H C L D EV LMGWVQ RRDHGGLIFVDLRDR+GLTQ+VF+P+V Sbjct: 2 LDSLDGMQRTHSCGGLRLDDLNKEVILMGWVQRRRDHGGLIFVDLRDREGLTQVVFNPEV 61 Query: 76 NPAAHERAHIIRSEYVLAIRGTVRPRPEGMTNPGMKTGEIEVYVSEWKLLNTSKTPAFVI 135 N AH +A I+RSE+V+AIRG V RPEGM NP + TGEIEV SE +LLNTS TP + + Sbjct: 62 NDLAHAKADILRSEFVIAIRGVVIARPEGMANPSLPTGEIEVAASELRLLNTSLTPPYEL 121 Query: 136 ED-RTEASENLRLQYRYLDLRRPRMANNFIVRHKAAQATRRYLDELGFLEIETPYLTKST 194 ED + + SE +RL+YRYLDLRRP + N +RH+AAQ R YL++ GF+E+ETP LT+ST Sbjct: 122 EDFKLDTSEAIRLRYRYLDLRRPGLMRNLRLRHRAAQVVRNYLNQQGFIEVETPVLTRST 181 Query: 195 PEGARDFLVPSRLNQGQFYALPQSPQLFKQLLMMSGMERYYQIVRCFRDEDMRADRQLEF 254 PEGARD+LVPSR N G+F+ALPQSPQLFKQLLMM+G+ERYYQ+ RCFRDED+RADRQ EF Sbjct: 182 PEGARDYLVPSRTNPGRFFALPQSPQLFKQLLMMAGLERYYQLCRCFRDEDLRADRQPEF 241 Query: 255 TQIDIEMSFVDEEQVMAMAEGLMARVFRDALDREIATPFPRMSYDDAMARYGVDKPDTRF 314 TQID+EMSF+ EE + + EG+MA +F++ L RE+ PFPR++Y + ++R+GVD+PD RF Sbjct: 242 TQIDMEMSFISEEDIYDVVEGMMAILFKEILGREVTLPFPRLTYAECISRFGVDRPDRRF 301 Query: 315 GLELQDVTHIVRGSNFKLFATAE----LVKAMRVPGGETMTRKEIDEFTEFVKIYGAQGL 370 GLEL +VT +V GS+F+ FA +VKA+ G + RKE+DE T FV IYGA+GL Sbjct: 302 GLELVEVTDLVAGSDFRTFADVAARGGVVKAINGKGLARLPRKELDELTGFVGIYGAKGL 361 Query: 371 AWIKIRPDEWQSPIAKFLSDEERAGLKDALGLETGDIVFFQAGAPGMVNAALGNLRVRLG 430 AWIK+ P WQSP+ KF + E++A + D L GD++ F A P +V+ ALG LR+ LG Sbjct: 362 AWIKLTPTGWQSPLTKFFTPEQQAAINDRLQARQGDLLMFVADIPQIVHTALGQLRLHLG 421 Query: 431 EHLGLIDENAFNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHMDVMVENPAAARARA 490 + LI ++F WVT FPL EYD EEKRYVA HHPFTSP + + ++ +P A RARA Sbjct: 422 KKEHLILPETYDFCWVTHFPLLEYDAEEKRYVAMHHPFTSPLEQDLPLLQTDPGAVRARA 481 Query: 491 YDMVLNGYELGGGSIRNHTAEKQRRMFAALGFSPEEAEAQFGFLTQALEMGAPPHGGIAF 550 YD+VLNG E+GGGSIR H + Q ++F L SPEEA+ +FGFL +ALE GAPPHGG+AF Sbjct: 482 YDLVLNGNEVGGGSIRIHQRQVQEKVFDTLKISPEEAQQKFGFLLEALEYGAPPHGGVAF 541 Query: 551 GMDRLAMLLTGSSSIRDVIAFPKTQKATCLLTQAPDSVSARQLRDLGLRL 600 G DRL M+L G+ SIR+VIAFPKTQKATCLLTQAP V QL +LG+RL Sbjct: 542 GFDRLVMILAGAKSIREVIAFPKTQKATCLLTQAPSEVDVAQLLELGIRL 591 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: 1026 Number of extensions: 23 Number of successful extensions: 3 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: 593 Length adjustment: 37 Effective length of query: 577 Effective length of database: 556 Effective search space: 320812 Effective search space used: 320812 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