Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_013537416.1 THEAM_RS03355 aspartate--tRNA ligase
Query= BRENDA::O32038 (592 letters) >NCBI__GCF_000185805.1:WP_013537416.1 Length = 596 Score = 678 bits (1750), Expect = 0.0 Identities = 333/588 (56%), Positives = 440/588 (74%), Gaps = 3/588 (0%) Query: 2 FGRTYYCGDITEKAIGESVTLKGWVQKRRDLGGLIFIDLRDRTGIVQVVFNPDVSKEALA 61 F RT+YCG+I+EK +G+ V + GWV RD GG++FIDLRDRTG VQVVF+P++SKE + Sbjct: 8 FKRTHYCGEISEKDLGKDVKVAGWVDTTRDHGGVVFIDLRDRTGKVQVVFSPEISKELVE 67 Query: 62 IAEGIRNEYVLDIQGKVVAREEGTVNPNLKTGAIEIHADGVNVLNAAKTPPFAISDQAEE 121 A+ +R+EYV+ ++G+V R EGT NP LKTG EI+A + +LN + PF I D + Sbjct: 68 KAKKLRHEYVVAVEGEVRRRPEGTENPKLKTGNYEIYAKKLQILNRSLPLPFPIEDNVK- 126 Query: 122 VSEDVRLKHRYLDLRRPAMFQTMQLRHNVTKAVRSFLDENGFLDIETPILTGSTPEGARD 181 VSE+VRLK+R+LDLRRP M + + RH + + VR +E GF+++ETP LT STPEGARD Sbjct: 127 VSEEVRLKYRFLDLRRPKMAENLLFRHRLYRVVREVFNEEGFVEVETPYLTKSTPEGARD 186 Query: 182 YLVPSRVHEGEFYALPQSPQLFKQLLMVSGIERYYQIARCFRDEDLRADRQPEFTQIDIE 241 +LVPSR++ G+FYALPQSPQLFKQ+LMV+GI+RYYQIARCFRDEDLRADRQPEFTQID E Sbjct: 187 FLVPSRIYPGKFYALPQSPQLFKQILMVAGIDRYYQIARCFRDEDLRADRQPEFTQIDFE 246 Query: 242 MSFMSQEDIMSLAEEMMAKVMRETKGEELQLPLPRMTYDEAMNKYGSDKPDTRFDMLLTD 301 MSF+++ D+M++AE+ + + +E G E+ +P MTYDEAM+++G+D+PDTRF + L + Sbjct: 247 MSFVAERDVMAVAEKFIRRAYKELLGIEIG-EIPVMTYDEAMSRFGTDRPDTRFGLELKE 305 Query: 302 VSDIVKDTEFKVFSSAVANGGVVKAINVKGGAGDYSRKDIDALGAFAANYGAKGLAWVKV 361 ++DI K FKVF S GG+VKA+N KGGA SRK+ID L F YGAKGLAW+KV Sbjct: 306 ITDIAKQCNFKVFRSVAEKGGIVKALNFKGGA-KLSRKEIDELTKFVGVYGAKGLAWIKV 364 Query: 362 EADGVKGPIAKFFDEEKQSKLIEALDAAEGDLLLFGADQFEVVAASLGALRLKLGKERGL 421 DG++ PI KFF E + +++++ L+A GD+L F AD+ EVV A+L LRLKLGK L Sbjct: 365 LPDGLQSPIVKFFTEGEMNEILKRLEAEVGDILFFVADKPEVVNAALANLRLKLGKMANL 424 Query: 422 IDEKLFNFLWVIDWPLLEHDPEEGRFYAAHHPFTMPVREDLELIETAPEDMKAQAYDLVL 481 IDE N LWV+D+P+ E + EE R+ A HHPFT P ED+E + P ++A+AYD+VL Sbjct: 425 IDESKVNILWVVDFPMFEWNEEEERWEALHHPFTSPKEEDIEKLLENPGAVRARAYDMVL 484 Query: 482 NGYELGGGSIRIFEKDIQEKMFALLGFSPEEAAEQFGFLLEAFEYGAPPHGGIALGLDRL 541 NG E+GGGSIRI +D+QEK+F ++G S EEA E+FGFLLEA +YGAPPHGG+A GLDRL Sbjct: 485 NGVEIGGGSIRIHREDVQEKVFKVIGLSEEEAKERFGFLLEALKYGAPPHGGMAFGLDRL 544 Query: 542 VMLLAGRTNLRDTIAFPKTASASCLMTEAPGEVSDAQLDELHLSIKKK 589 ++ G ++RD IAFPKT CL+T AP V + QLDELH+ +K K Sbjct: 545 CAIMRGEESIRDVIAFPKTQRGQCLLTGAPDTVREEQLDELHIEVKTK 592 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: 1004 Number of extensions: 45 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: 592 Length of database: 596 Length adjustment: 37 Effective length of query: 555 Effective length of database: 559 Effective search space: 310245 Effective search space used: 310245 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 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