Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate WP_013450995.1 CALNI_RS04355 aspartate--tRNA ligase
Query= uniprot:SYDND_DESVH (610 letters) >NCBI__GCF_000183405.1:WP_013450995.1 Length = 596 Score = 696 bits (1795), Expect = 0.0 Identities = 334/586 (56%), Positives = 430/586 (73%), Gaps = 4/586 (0%) Query: 19 LGDWQRTHSCCELTAADVGNDVCIMGWVQYRRDHGGLIFVDLRDRKGLTQVVFSPDFAPE 78 LGDW+RTH C EL + G D+C+MGWV RRDHGG+IF+DLRD+ GL Q+V +P+ +PE Sbjct: 5 LGDWRRTHYCGELNGKNTGEDICVMGWVHRRRDHGGVIFIDLRDKTGLLQLVLNPEISPE 64 Query: 79 AHKDAHIVRSEYVLAIRGRVRPRPEGMTNPGMKTGEIEVVVSEWKLLNTSKTPPFLIEDR 138 AH A VRSEYV+A++G+V RPEG N + TGEIE++V E K+LN +KTPPF IE+ Sbjct: 65 AHSIAEAVRSEYVVAVKGKVEKRPEGTINENLPTGEIEIIVKEIKILNNAKTPPFQIEEN 124 Query: 139 TEASENLRLAWRYLDLRRPRMARNFMLRHRAAQSARRYLDELDFLEIETPYLTKATPEGA 198 T E++RL +RYLDLRRP + +N +LRH ++ R YL FL+IETP+LTK+TPEGA Sbjct: 125 TNVGEDVRLKYRYLDLRRPNLQKNIILRHNLTRTMREYLYGKGFLDIETPFLTKSTPEGA 184 Query: 199 RDFLVPSRLNHGMFYALPQSPQIFKQLLMVSGMDRYYQIVRCFRDEDMRADRQLEFTQID 258 RD+LVPSR+N G FYALPQSPQ+FKQLLM+SG DRY+QIVRCFRDED+RADRQ EFTQ+D Sbjct: 185 RDYLVPSRVNPGKFYALPQSPQMFKQLLMISGYDRYFQIVRCFRDEDLRADRQPEFTQLD 244 Query: 259 IEMSFVDEERVMSMAEGLMSRVMKDTLGVDVTVPFPRMTYDQAMGEYGVDKPDTRFDLRL 318 +EMSF+D + +M + EGL + + G+ V PFP MTY +AM +Y D PDTRF+L Sbjct: 245 MEMSFIDRQDLMDLIEGLFVEIFQKVAGITVQRPFPVMTYAEAMEKYSHDAPDTRFELFT 304 Query: 319 KDVTDAVRGSEFKLFAKA----PLVKAMRVPGGETMTRKEIDEFTEFVKIYGAQGLAWIK 374 K + D V+ EFK+F A +VKA+ G +RKEIDE T++ GA+GLA+IK Sbjct: 305 KTINDLVKDCEFKVFTDAIKEGGIVKAINAKGAGKFSRKEIDEITDYAVSLGAKGLAYIK 364 Query: 375 IREGEWQSPIAKFLSEAERAALVAALGLEVGDIVFFQAGEPGMVNAALGNLRVKLGQHLG 434 I E QSPI KFL E ++ + +VGDIVFF AGE VN + +R++LG+ LG Sbjct: 365 INEDGLQSPIIKFLGEQLTHRILDTMDAKVGDIVFFGAGEKSTVNLFMSKVRLELGRRLG 424 Query: 435 LIPEDTYNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHFDLMTSDPAAARARAYDMV 494 LI ++ YNF WV DFPL E+D+EEKRY A HHPFT+P D L +DP RA+AYD+V Sbjct: 425 LIDKNKYNFTWVIDFPLLEWDKEEKRYAAVHHPFTAPVDEDIPLFDTDPLKIRAKAYDLV 484 Query: 495 LNGYELGGGSIRIHSAEVQRRMFAALGLDPQEAEEKFGFLIQALEHGAPPHGGIAFGMDR 554 LNG E+GGGSIRIH +++Q +MF LGL +E + KFGF I+AL +G PPHGGIAFG+DR Sbjct: 485 LNGSEIGGGSIRIHRSDIQEKMFNILGLTKEECDLKFGFFIEALRYGTPPHGGIAFGVDR 544 Query: 555 LVMLLTGSPSIRDVIAFPKTQKATCLMTQAPDAVSARQLRDLGIRL 600 + +L G+ SIRDVIAFPKTQKATCLM+ AP+ V A+QL++L I+L Sbjct: 545 IASILAGADSIRDVIAFPKTQKATCLMSDAPNKVDAKQLKELSIKL 590 Lambda K H 0.322 0.138 0.415 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: 1027 Number of extensions: 30 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: 610 Length of database: 596 Length adjustment: 37 Effective length of query: 573 Effective length of database: 559 Effective search space: 320307 Effective search space used: 320307 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