Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate WP_013257702.1 DEBA_RS04405 aspartate--tRNA ligase
Query= uniprot:SYDND_DESVH (610 letters) >NCBI__GCF_000143965.1:WP_013257702.1 Length = 595 Score = 681 bits (1757), Expect = 0.0 Identities = 337/587 (57%), Positives = 438/587 (74%), Gaps = 6/587 (1%) Query: 21 DWQRTHSCCELTAADVGNDVCIMGWVQYRRDHGGLIFVDLRDRKGLTQVVFSPDFAPEAH 80 D +RTH+C +LTAADVG V +MGW Q RRDHGGLIFVDLRDR GLTQVVF+P+ + +H Sbjct: 8 DLKRTHTCGQLTAADVGKQVVLMGWCQRRRDHGGLIFVDLRDRDGLTQVVFNPEVSGGSH 67 Query: 81 KDAHIVRSEYVLAIRGRVRPRPEGMTNPGMKTGEIEVVVSEWKLLNTSKTPPFLIEDRTE 140 AH +R+EY LA++G+V RPEGM N + TG +EV VS++++LN SKTPPF++ED + Sbjct: 68 SLAHAIRNEYCLALQGKVDLRPEGMQNDKLGTGAVEVYVSDFEILNASKTPPFMLEDWID 127 Query: 141 ASENLRLAWRYLDLRRPRMARNFMLRHRAAQSARRYLDELDFLEIETPYLTKATPEGARD 200 E +RL +RYLDLRR + RN LRH+AAQ+AR YL++ FLE+ETP+LTK+TPEGARD Sbjct: 128 VGEAVRLKYRYLDLRRQVVFRNLKLRHQAAQAARGYLNDQGFLEVETPFLTKSTPEGARD 187 Query: 201 FLVPSRLNHGMFYALPQSPQIFKQLLMVSGMDRYYQIVRCFRDEDMRADRQLEFTQIDIE 260 +LVPSR+ G FYALPQSPQ+FKQLLMV G++RYYQIV+CFRDED+RADRQ EFTQ+D+E Sbjct: 188 YLVPSRVQRGRFYALPQSPQLFKQLLMVGGVERYYQIVKCFRDEDLRADRQPEFTQVDLE 247 Query: 261 MSFVDEERVMSMAEGLMSRVMKDTLGVDVTVPFPRMTYDQAMGEYGVDKPDTRFDLRLKD 320 MSFVDE VM + EGL+ ++K T GV++ P PR++Y QAM +G+D PD RF L L D Sbjct: 248 MSFVDENDVMDLTEGLVGAILKATRGVELG-PVPRLSYAQAMERFGLDAPDIRFGLELTD 306 Query: 321 VTDAVRGSEFKLFAKA----PLVKAMRVPGGETMTRKEIDEFTEFVKIYGAQGLAWIKIR 376 + + ++ ++FK+F A +VKA+ G ++RK++D+ T FV YGA+GLAW+K++ Sbjct: 307 LGELMQKTQFKVFRGAIDGGGVVKAINGKGMGGLSRKDLDDLTAFVADYGAKGLAWVKLK 366 Query: 377 E-GEWQSPIAKFLSEAERAALVAALGLEVGDIVFFQAGEPGMVNAALGNLRVKLGQHLGL 435 + G+WQSPIAKF+ +AA+ + E GDI+FF A + +V+ +LG LR++L + L Sbjct: 367 DGGQWQSPIAKFIEPEVQAAINERMAAEDGDILFFGADKKPVVSESLGRLRLELSRRFQL 426 Query: 436 IPEDTYNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHFDLMTSDPAAARARAYDMVL 495 D F WVTDFP+FEYD +EKRY A HHPFTSPK D M SDP A ARAYD+VL Sbjct: 427 TSPDDLRFCWVTDFPMFEYDPQEKRYNAMHHPFTSPKSEFEDKMGSDPEACLARAYDLVL 486 Query: 496 NGYELGGGSIRIHSAEVQRRMFAALGLDPQEAEEKFGFLIQALEHGAPPHGGIAFGMDRL 555 NG E+GGGSIRIH E Q ++F AL +D ++A EKFGFL+ AL GAPPHGG+A G DRL Sbjct: 487 NGSEVGGGSIRIHRPETQAKVFGALNIDDEQAREKFGFLLDALAFGAPPHGGLALGFDRL 546 Query: 556 VMLLTGSPSIRDVIAFPKTQKATCLMTQAPDAVSARQLRDLGIRLRE 602 V +L G SIR+VIAFPKTQKA+C MT AP V QL +LG+R+ + Sbjct: 547 VAILAGQGSIREVIAFPKTQKASCPMTDAPSTVDRNQLLELGLRVEK 593 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: 1044 Number of extensions: 41 Number of successful extensions: 4 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: 595 Length adjustment: 37 Effective length of query: 573 Effective length of database: 558 Effective search space: 319734 Effective search space used: 319734 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