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 SMc03173 SMc03173 lysyl-tRNA synthetase
Query= curated2:Q980V3 (429 letters) >FitnessBrowser__Smeli:SMc03173 Length = 498 Score = 117 bits (293), Expect = 8e-31 Identities = 136/450 (30%), Positives = 206/450 (45%), Gaps = 52/450 (11%) Query: 16 GSEVKVAGWVHNVRNLGGKIFILLRDKSGIGQIVVEKGN---NAYDKVINIGLESTIVVN 72 G V VAG V + RN G +F+ L D SG QI K A + I L I V Sbjct: 60 GETVTVAGRVFSSRNSG--MFMDLHDASGKIQIFSHKDTAPEEARALLPMIDLGDIIGVT 117 Query: 73 GVVKADARAPNGVEVHAKDIEILSYARSPLPLDVTGKVKADIDTRLRERLLDLRRLEMQA 132 G V+ R + V+AK+I +L + P+P G ADI+TR R+R LD+ E ++ Sbjct: 118 GEVRRTKRGE--LTVNAKEITMLCKSLLPMPEKYHGL--ADIETRYRKRYLDIMVNE-ES 172 Query: 133 VLKIQ--SVAVKSFRETLYKHGFVEVFTPKIIASATEGGAQLFPVLYFGK----EAFLAQ 186 L+ Q S V S R L GF+EV TP + GGA P + +L Sbjct: 173 KLRFQQRSRIVSSLRRFLEDEGFMEVETPML--QPIYGGATAEPFKTHHNTLKLDMYLRI 230 Query: 187 SPQLYKE--LLAGAIERVFEIAPAWRAEESDTPYHLSEFISMDVEMAFADYNDIMALIEQ 244 +P+LY + L++G ++VFEI +R E T H EF M+ A+ADY D+M L+E+ Sbjct: 231 APELYLKRILVSGLTDKVFEINRNFRNEGVSTR-HNPEFTMMECYWAYADYEDVMGLVER 289 Query: 245 IIYNMINDVKRECENEL--KILNYTPPNVRIPIKKV-------------SYSDAIELLKS 289 + + V + E E K L++ P R+ + S +A + + Sbjct: 290 MFETLALAVHGKTEFEFGDKQLSFKGPFPRVSMPAAVKDATGIDFLALKSDEEARQAARD 349 Query: 290 KGVNIKFGDDIGTPELRVLYNELKEDLYF----VTDWPWLSRPFYTKQKKDNPQLSESFD 345 GV I+ D L L+ E E V +P PF K+ P+L E F+ Sbjct: 350 AGVEIE-KDATWGEVLAFLFEEKVEATLIQPAHVIHFPKDISPF-AKEVPGEPRLVERFE 407 Query: 346 LIFRWLEIVSGSS--------RNHVKEVLENSLKVRGLNPESF-EFFLKWFDYGMPPHAG 396 EI + S R + E +E + RG ++ E FL D GMPP G Sbjct: 408 TYCNGWEIGNAFSELNDPVEQRARMVEQMEQA-HARGEKEKTLDEDFLDAMDQGMPPAGG 466 Query: 397 FGMGLARVMLMLTGLQSVKEVVPFPRDKKR 426 G+G+ R++++LT S+++++ FP +++ Sbjct: 467 LGIGVDRLIMLLTNSPSIRDIILFPARRQK 496 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: 429 Number of extensions: 29 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: 498 Length adjustment: 33 Effective length of query: 396 Effective length of database: 465 Effective search space: 184140 Effective search space used: 184140 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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