Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23 (characterized, see rationale)
to candidate WP_012675723.1 PERMA_RS00450 aspartate--tRNA ligase
Query= uniprot:SYDND_DESVH (610 letters) >NCBI__GCF_000021565.1:WP_012675723.1 Length = 605 Score = 648 bits (1672), Expect = 0.0 Identities = 330/600 (55%), Positives = 429/600 (71%), Gaps = 13/600 (2%) Query: 19 LGDWQRTHSCCELTAADVGNDVCIMGWVQYRRDHGGLIFVDLRDRKGLTQVVFSPDFAP- 77 LGD++R + C ELT ++G++V ++GW RDHGG+IF++LRD++G+ QVV P +P Sbjct: 5 LGDFKRDYFCGELTENNIGDEVRLLGWADSVRDHGGVIFINLRDKEGIIQVVIDPSKSPK 64 Query: 78 EAHKDAHIVRSEYVLAIRGRVRPRPEGMTNPGMKTGEIEVVVSEWKLLNTSKTPPFLIED 137 EA++ A VRSEYVLA+RGRV+ RP G NP + TG IE+ V E ++LNT PF IED Sbjct: 65 EAYEKAKKVRSEYVLAVRGRVQRRPAGTENPKLPTGTIEIAVDELRILNTCDILPFPIED 124 Query: 138 RTEASENLRLAWRYLDLRRPRMARNFMLRHRAAQSARRYLDELDFLEIETPYLTKATPEG 197 A E +RL +R+LD+RRP M + +LRH Q+ R YL FLE+ETP LTK+TPEG Sbjct: 125 GISAHEEVRLRYRFLDIRRPEMMKKLILRHEVYQATREYLAGHGFLEVETPMLTKSTPEG 184 Query: 198 ARDFLVPSRLNHGMFYALPQSPQIFKQLLMVSGMDRYYQIVRCFRDEDMRADRQLEFTQI 257 ARDFLVP+RL G FYALPQSPQ+FKQ+LMVSG+DRY+QIV+CFRDED+R DRQ EFTQI Sbjct: 185 ARDFLVPARLEKGKFYALPQSPQLFKQILMVSGIDRYFQIVKCFRDEDLRKDRQPEFTQI 244 Query: 258 DIEMSFVDEERVMSMAEGLMSRVMKDTLGVDVTVPFPRMTYDQAMGEYGVDKPDTRFDLR 317 D EMSFVDEE V++++EGL+ + K LG+++ +PF RM+Y +A+ YG DKPD R+ L Sbjct: 245 DFEMSFVDEEDVITVSEGLIHYIFKKVLGIELKLPFKRMSYTEAIERYGTDKPDLRYSLE 304 Query: 318 LKDVTDAVRGSEFKLF----AKAPLVKAMRVPGGETMTRKEIDEFTEFVKIYGAQGLAWI 373 LKD+TD + +FK+F K +VK + V GG +RKEID+ TE K YGA+G+AWI Sbjct: 305 LKDITDIAKDVQFKVFKDTVEKGGIVKGINVKGGSKFSRKEIDDLTEEAKKYGAKGMAWI 364 Query: 374 KIRE-GEWQSPIAKFLSEAERAALVAALGLEVGDIVFFQAGEPGMVNAALGNLRVKLGQH 432 KI E G QSPI KF +E + + + E GD++ F A + + LG LR L + Sbjct: 365 KINEDGSLQSPIVKFFTEEQINKIKEIMEGENGDLLIFIADSYEITHRVLGFLRKHLAEK 424 Query: 433 LGLIPEDTYNFLWVTDFPLFEYDEEEKRYVACHHPFTSPKDGHFDLM---TSDPAAA--- 486 L LIPE+ + F+WV DFPL E+DEEE R VA HHPFTSPK+ D + D A Sbjct: 425 LKLIPENVWEFVWVVDFPLVEWDEEEGRLVALHHPFTSPKEEDIDRLDEAIQDKKVALSF 484 Query: 487 RARAYDMVLNGYELGGGSIRIHSAEVQRRMFAALGLDPQEAEEKFGFLIQALEHGAPPHG 546 R+RAYD+VLNG E+GGGSIRIHS+ +Q+++F LG+ +EAEEKFGFLI AL++GAPPHG Sbjct: 485 RSRAYDLVLNGEEIGGGSIRIHSSHIQKKVFELLGISDEEAEEKFGFLINALKYGAPPHG 544 Query: 547 GIAFGMDRLVMLLTGSPSIRDVIAFPKTQKATCLMTQAPDAVSARQLRDLGIRLRETPQE 606 G+AFG+DR+V L+TGS SIRDVIAFPKTQK C +T APD V QL +LGI + P+E Sbjct: 545 GLAFGLDRIVALMTGSESIRDVIAFPKTQKGICPLTDAPDFVQEDQLEELGIEV-NIPEE 603 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: 1033 Number of extensions: 39 Number of successful extensions: 5 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: 605 Length adjustment: 37 Effective length of query: 573 Effective length of database: 568 Effective search space: 325464 Effective search space used: 325464 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