Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_017548732.1 C792_RS0106905 aspartate--tRNA ligase
Query= BRENDA::O32038 (592 letters) >NCBI__GCF_000330705.1:WP_017548732.1 Length = 585 Score = 758 bits (1956), Expect = 0.0 Identities = 373/577 (64%), Positives = 454/577 (78%), Gaps = 2/577 (0%) Query: 10 DITEKAIGESVTLKGWVQKRRDLGGLIFIDLRDRTGIVQVVFNPDVSKEALAIAEGIRNE 69 ++TE GE VTLKGWVQKRRDLGGLIFIDLRDR G++QVVFNP++SKEAL AE IR+E Sbjct: 7 EVTESQTGEKVTLKGWVQKRRDLGGLIFIDLRDRKGVIQVVFNPEISKEALETAERIRSE 66 Query: 70 YVLDIQGKVVAREEGTVNPNLKTGAIEIHADGVNVLNAAKTPPFAISDQAEEVSEDVRLK 129 YV+++ G+V+ R+ VN N+ TG IEI AD V VL+ A+TPPF I D + + EDVRLK Sbjct: 67 YVIEVSGEVLKRDPSQVNENIATGKIEILADEVTVLSKAETPPFQILD--DSIGEDVRLK 124 Query: 130 HRYLDLRRPAMFQTMQLRHNVTKAVRSFLDENGFLDIETPILTGSTPEGARDYLVPSRVH 189 +RY DLRR + T++LRH + ++VR+FLD F+DIETP+L+ STPEGARDYLVPSRVH Sbjct: 125 YRYFDLRRNKLQNTLRLRHQINRSVRNFLDNEEFVDIETPVLSKSTPEGARDYLVPSRVH 184 Query: 190 EGEFYALPQSPQLFKQLLMVSGIERYYQIARCFRDEDLRADRQPEFTQIDIEMSFMSQED 249 EGEFYALPQSPQ++KQLLM+SG+E+YYQI +CFRDEDLRADRQPEFTQIDIEMSFM QE Sbjct: 185 EGEFYALPQSPQIYKQLLMLSGMEKYYQIVKCFRDEDLRADRQPEFTQIDIEMSFMDQEQ 244 Query: 250 IMSLAEEMMAKVMRETKGEELQLPLPRMTYDEAMNKYGSDKPDTRFDMLLTDVSDIVKDT 309 IM L E ++ VM+ KG ++ LP+PRMTY++AM +YG DKPDTRF + L D+S+ + Sbjct: 245 IMELNERLIRHVMKTVKGVDIALPIPRMTYEQAMAEYGIDKPDTRFGLKLNDLSEFSRTV 304 Query: 310 EFKVFSSAVANGGVVKAINVKGGAGDYSRKDIDALGAFAANYGAKGLAWVKVEADGVKGP 369 +FKVF S V NGG+VKAI VKG A +SRKDID L A+ YGAKGLAW+KV+ + GP Sbjct: 305 DFKVFRSTVENGGMVKAIVVKGEADSFSRKDIDKLEAYVKTYGAKGLAWLKVKDGALNGP 364 Query: 370 IAKFFDEEKQSKLIEALDAAEGDLLLFGADQFEVVAASLGALRLKLGKERGLIDEKLFNF 429 IAKFF+E+ Q +L E L +GDL LF AD +VV ASLG LR KL K+ LI+ +NF Sbjct: 365 IAKFFNEDNQKELSETLGLEDGDLTLFVADSAKVVHASLGNLRNKLAKDLDLIEADQYNF 424 Query: 430 LWVIDWPLLEHDPEEGRFYAAHHPFTMPVREDLELIETAPEDMKAQAYDLVLNGYELGGG 489 LWV DWPL E+D E GR++AAHHPFT P ED+EL+ET PE +KA AYD+VLNGYELGGG Sbjct: 425 LWVTDWPLFEYDEEAGRYFAAHHPFTSPKAEDVELLETEPEKVKANAYDIVLNGYELGGG 484 Query: 490 SIRIFEKDIQEKMFALLGFSPEEAAEQFGFLLEAFEYGAPPHGGIALGLDRLVMLLAGRT 549 SIRI + +Q+KMF LGF+ EE EQFGFL+EAF+YGAPPHGGIA GLDRLVMLLAG Sbjct: 485 SIRIHDAQMQQKMFRALGFTDEERDEQFGFLIEAFKYGAPPHGGIAYGLDRLVMLLAGTD 544 Query: 550 NLRDTIAFPKTASASCLMTEAPGEVSDAQLDELHLSI 586 N+RD IAFPKTASA+ LM AP EV+ AQL ELH+ + Sbjct: 545 NIRDVIAFPKTASAADLMMSAPSEVAKAQLKELHIEL 581 Lambda K H 0.319 0.137 0.394 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: 965 Number of extensions: 34 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: 592 Length of database: 585 Length adjustment: 37 Effective length of query: 555 Effective length of database: 548 Effective search space: 304140 Effective search space used: 304140 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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