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_028950302.1 Q385_RS0103300 lysine--tRNA ligase
Query= curated2:Q980V3 (429 letters) >NCBI__GCF_000619805.1:WP_028950302.1 Length = 577 Score = 138 bits (348), Expect = 4e-37 Identities = 136/444 (30%), Positives = 207/444 (46%), Gaps = 48/444 (10%) Query: 16 GSEVKVAGWVHNVRNLGGKIFILLRDKSGIGQIVVEK---GNNAYDKVIN-IGLESTIVV 71 G EV VAG + +R+ G F L+D G QI G Y K + I + I V Sbjct: 137 GKEVAVAGRLVALRDQGKAAFGHLQDADGKLQIYFNADILGQENYQKAMELIDIGDIIGV 196 Query: 72 NGVVKADARAPNGVEVHAKDIEILSYARSPLPLDVTGKVKADIDTRLRERLLDL-RRLEM 130 G VEVH+ ++LS + PLP G DI+ R R R LDL Sbjct: 197 KGKFFRTMTGELTVEVHS--YQMLSKSLRPLPEKWHGL--KDIEERYRYRFLDLIANQRS 252 Query: 131 QAVLKIQSVAVKSFRETLYKHGFVEVFTPKIIASATEGGAQLFPVLYFGK----EAFLAQ 186 + + K++S A+KS RE L GF+EV TP I GA P + + +L Sbjct: 253 REIFKLRSKAIKSLREFLESKGFIEVETP--ILQPVASGALAKPFITYHNALDMNLYLRI 310 Query: 187 SPQLY-KELLAGAIERVFEIAPAWRAEESDTPYHLSEFISMDVEMAFADYNDIMALIEQI 245 +P+LY K L+ G RVFEI +R E DT H EF ++ A+ DYND+MAL E++ Sbjct: 311 APELYLKMLVVGGFNRVFEIGRNFRNEGIDTT-HNPEFTMVEFYAAYLDYNDLMALTEEL 369 Query: 246 IYNMINDV--KRECENELKILNYTPPNVRIPI-----KKVSYSDAIELLKSKGVNIKFGD 298 ++ D + + E + +++ P R+P +K L K N F Sbjct: 370 FRKILLDTVGTLKIKWEDQEIDFEKPFRRLPFFEALKQKTGKDKEFFLDYEKAKN--FAK 427 Query: 299 DIGTPELRVLYNE----------LKEDLY---FVTDWPWLSRPFYTKQKKDNPQLSESFD 345 ++G P+ L + ++EDL FV D+P + P K +++P L E F+ Sbjct: 428 EVGIPKADTLTHMKILDKLFEHFVEEDLVQPTFVIDFPKILSPL-AKTHRNDPDLVERFE 486 Query: 346 LIFRWLEIVSGSSRNH----VKEVLENSLKVRGLNPESF----EFFLKWFDYGMPPHAGF 397 LI E+ + + + +E ++ + + E E FL +YG+PP AG Sbjct: 487 LIINKQELANAYTELNDPFDQRERFIQQIREKEMGDEEAMDVDETFLTALEYGLPPTAGE 546 Query: 398 GMGLARVMLMLTGLQSVKEVVPFP 421 G+G+ R+++MLT S++EV+ FP Sbjct: 547 GIGIDRLVMMLTDSVSIREVILFP 570 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: 588 Number of extensions: 35 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: 577 Length adjustment: 34 Effective length of query: 395 Effective length of database: 543 Effective search space: 214485 Effective search space used: 214485 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