Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_012103469.1 CKL_RS15210 aspartate--tRNA ligase
Query= BRENDA::Q9KDG1 (595 letters) >NCBI__GCF_000016505.1:WP_012103469.1 Length = 590 Score = 633 bits (1632), Expect = 0.0 Identities = 302/583 (51%), Positives = 427/583 (73%), Gaps = 4/583 (0%) Query: 4 RTHHCGQLSEEQVNERVQLKGWVQRRRDLGQVIFVDLRDRSGVVQLVFNSDISQEALETA 63 RT CG L+E + +++ + GWVQR+R+LG ++FVDLRDR+G++Q+VF I++EA E + Sbjct: 10 RTCMCGGLTEANIGDKITVMGWVQRKRNLGGLVFVDLRDRTGILQIVFGEAINKEAFEKS 69 Query: 64 EKVRNEYVLDVEGVVLKRDPSTVNDKIATGTIEVHVERLTILNKAKSLPFQIEANTDASE 123 + V++EY + G ++KR+ + N +I TG +E+ E + I +++++ P I+ N DA+E Sbjct: 70 DSVKSEYCIAAVGTIVKRE--SPNMEIPTGMVELKGEYIKIFSESETPPIYIKENLDAAE 127 Query: 124 DIRLKYRYLDLRRPDMQETMKLRHQTTKLIRDFLDGQEFFEIETPMLTKSTPEGARDYLV 183 +IRLKYRYLDLRRPDMQ LRH+T K+IRDFLD Q F EIETP+L KSTPEGARDYLV Sbjct: 128 NIRLKYRYLDLRRPDMQRIFMLRHKTAKVIRDFLDEQGFLEIETPILGKSTPEGARDYLV 187 Query: 184 PSRVHHGEFYALPQSPQIFKQLLMVSGFERYYQIVRCFRDEDLRADRQPEFTQIDIETSF 243 PSR + G++YALPQSPQ+FKQLLMVSG++RY+QI +CFRDEDLRA+RQPEFTQ+D+E SF Sbjct: 188 PSRNYKGKYYALPQSPQLFKQLLMVSGYDRYFQIAKCFRDEDLRANRQPEFTQVDMEISF 247 Query: 244 MDKEDLLTMTENMMAKIMKEVKGLDVALPFPRMTYDDAMNRYGSDKPDTRFEMELIELSD 303 +D+E+++ + E ++ ++ K++ +DV LP RMTY AM++YGSDKPD RF ME+ ++S+ Sbjct: 248 VDQEEVMDLNERLIQRVFKQILDVDVKLPIERMTYKTAMDKYGSDKPDLRFGMEINDISE 307 Query: 304 IVKDSDFKVFSSAIKSGGIVKGLNLKGGAGSLSRKEIDGLAEFVKPYGAKGLAWLKVEEG 363 +VK DFKVF +A+++GG V+ + + G A +L RK++D L EFVK YGA GL W+ ++ Sbjct: 308 VVKGVDFKVFQNALENGGSVRAIKVTGSA-ALGRKQLDKLVEFVKTYGASGLIWMAYKKE 366 Query: 364 ELKGPIAKFFAGETGAELQQAMGAEDGDLLFFAADKKEVVFDSLGALRLKLGKDFNLID- 422 +K I+KF E + M A +GDL+ ADK +VVF+SLGALR+ + K +++ Sbjct: 367 GIKCSISKFLTEEDTQNILNKMEAAEGDLILIVADKNKVVFESLGALRIHMAKQTGILEG 426 Query: 423 ESKFNFLWVVDFPLVEYDEEAKRFVALHHPFTSPKQEDLTKLETDPASVRADAYDLVLNG 482 + F F+W+ +FPL+ Y+EE R+ A HHPF P ED+ LE++P VRA AYD+VLNG Sbjct: 427 NNDFKFVWITEFPLLSYNEEENRYQAEHHPFVMPMDEDIQYLESNPEKVRAKAYDIVLNG 486 Query: 483 YELGGGSQRIYQRPVQEKMFAALGFTEEAAQKEFGFLLEAFEYGTPPHGGIALGLDRLVM 542 ELGGGS RI+ +QEKMF A+G +++ A +FG+ LEA ++G PPHGG+A G DR++M Sbjct: 487 EELGGGSIRIHDTKLQEKMFGAIGISKDTAWNKFGYFLEALKFGPPPHGGLAYGFDRMIM 546 Query: 543 LLAGRLNLRDTIAFPKTASASCLLTEAPGEVSLEQLLDLNLSI 585 LAG N++D IAFPK +A C LTEAP V QL DL + + Sbjct: 547 FLAGTDNIKDVIAFPKNQNAFCPLTEAPNSVDKSQLKDLGIEV 589 Lambda K H 0.319 0.138 0.393 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: 957 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: 595 Length of database: 590 Length adjustment: 37 Effective length of query: 558 Effective length of database: 553 Effective search space: 308574 Effective search space used: 308574 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