Align Aspartate--tRNA(Asp/Asn) ligase; EC 6.1.1.23; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS (uncharacterized)
to candidate WP_012675654.1 PERMA_RS07070 lysine--tRNA ligase
Query= curated2:Q980V3 (429 letters) >NCBI__GCF_000021565.1:WP_012675654.1 Length = 579 Score = 135 bits (340), Expect = 3e-36 Identities = 134/452 (29%), Positives = 217/452 (48%), Gaps = 48/452 (10%) Query: 7 VSELNPKLDGSEVKVAGWVHNVRNLGGKIFILLRDKSGIGQIVVEK---GNNAYDKVINI 63 V +L+P + +V VAG + + R+ G F ++D G QI + G+ Y++ + I Sbjct: 132 VYDLDPGRE--KVSVAGRIVSFRDQGKAAFGHIQDADGKIQIYFRRDTLGDEKYNEAMEI 189 Query: 64 GLESTIVVNGVVKADARAPNG-VEVHAKDIEILSYARSPLPLDVTGKVKADIDTRLRERL 122 IV GV R G + V KD ++L+ + LP G D++ R R R Sbjct: 190 LDIGDIV--GVEGELFRTMTGELTVEVKDFKLLTKSLRALPEKWHGL--KDVELRYRRRY 245 Query: 123 LDL-RRLEMQAVLKIQSVAVKSFRETLYKHGFVEVFTPKIIASATEGGAQLFPVLYFGK- 180 +DL + + + KI+ A+KS RE L GF+EV TP I + GA P + Sbjct: 246 VDLIANPKAREIFKIRYKAIKSLREFLESEGFMEVETP--ILQSVASGAMARPFITHHNA 303 Query: 181 ---EAFLAQSPQLY-KELLAGAIERVFEIAPAWRAEESDTPYHLSEFISMDVEMAFADYN 236 + +L +P+LY K L+ G RV+E+ +R E DT H EF ++ A+ DYN Sbjct: 304 LDIDMYLRIAPELYLKMLIVGGFNRVYELGRNFRNEGIDTT-HNPEFTMVEFYAAYMDYN 362 Query: 237 DIMALIEQIIYNMINDV--KRECENELKILNYTPPNVRI----PIKKVSYSDAIELLKSK 290 D+M L E+++ ++ D K + E + L+++ P R+ +K+ + D E + Sbjct: 363 DLMDLTERLMRKILMDTVGKLKITWEGQELDFSKPFRRLRFFDALKEKTGKDK-EFFLDE 421 Query: 291 GVNIKFGDDIGTPELRVLYNE----------LKEDLY---FVTDWPWLSRPFYTKQKKDN 337 G +F ++G P+ L + ++EDL FV D+P + P K +D+ Sbjct: 422 GKAREFAKEVGIPKAETLTHLKILDKLFEHFIEEDLVQPTFVIDFPKILSPL-AKTHRDD 480 Query: 338 PQLSESFDLIFRWLEIVSGSSR----NHVKEVLENSLKVRGLNPESF----EFFLKWFDY 389 P L E F+LI EI + + +E LK + E E FL +Y Sbjct: 481 PDLVERFELIVNKQEIANAYTELNDPEDQRERFLQQLKEKAAGDEEAMDIDENFLTALEY 540 Query: 390 GMPPHAGFGMGLARVMLMLTGLQSVKEVVPFP 421 G+PP G G+G+ R+++MLT S++EV+ FP Sbjct: 541 GLPPTGGEGIGIDRLVMMLTDSPSIREVILFP 572 Lambda K H 0.320 0.138 0.404 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: 595 Number of extensions: 33 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: 429 Length of database: 579 Length adjustment: 34 Effective length of query: 395 Effective length of database: 545 Effective search space: 215275 Effective search space used: 215275 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 (21.8 bits) S2: 52 (24.6 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