Align aspartate-tRNAAsn ligase (EC 6.1.1.23) (characterized)
to candidate WP_025274508.1 HALAL_RS0113505 aspartate--tRNA ligase
Query= BRENDA::Q9KDG1 (595 letters) >NCBI__GCF_000527155.1:WP_025274508.1 Length = 591 Score = 564 bits (1453), Expect = e-165 Identities = 296/578 (51%), Positives = 392/578 (67%), Gaps = 10/578 (1%) Query: 4 RTHHCGQLSEEQVNERVQLKGWVQRRRDLGQVIFVDLRDRSGVVQLVFNSDISQEALETA 63 RTH G L E ++ V L GWV RRRD G V FVDLRD SGVVQ+VF EA E A Sbjct: 3 RTHRAGTLRAEHADQEVTLAGWVARRRDHGGVEFVDLRDSSGVVQIVFRDS---EAAEAA 59 Query: 64 EKVRNEYVLDVEGVVLKRDPSTVNDKIATGTIEVHVERLTILNKAKSLPFQIEANTDASE 123 +K+RNEY + + G V R N +I TG+IEV V LT+L+ A+ LPFQI+ + D SE Sbjct: 60 QKLRNEYCIQITGTVAIRPDGNENPEIPTGSIEVSVADLTVLSVAEPLPFQIDDHIDVSE 119 Query: 124 DIRLKYRYLDLRRPDMQETMKLRHQTTKLIRDFLDGQEFFEIETPMLTKSTPEGARDYLV 183 ++RL YRYLDLRR ++ R Q TK+ RD L ++F E+ETP LT+STPEGARD+LV Sbjct: 120 EVRLHYRYLDLRRSGPSRALRTRSQATKIARDILAEEDFLEVETPTLTRSTPEGARDFLV 179 Query: 184 PSRVHHGEFYALPQSPQIFKQLLMVSGFERYYQIVRCFRDEDLRADRQPEFTQIDIETSF 243 P R+ G +YALPQSPQ+FKQLLMV GFERYYQI RC+RDED RADRQPEFTQ+DIE +F Sbjct: 180 PVRLQPGSWYALPQSPQLFKQLLMVGGFERYYQIARCYRDEDFRADRQPEFTQLDIEAAF 239 Query: 244 MDKEDLLTMTENMMAKIMKEVKGLDVALPFPRMTYDDAMNRYGSDKPDTRFEMELIELSD 303 + +ED++++ E ++A + KE+ D+ P P +T+ +AMNR+GSDKPD RF EL EL+D Sbjct: 240 VSQEDIISIGEKIVAGLWKELADYDIPTPIPHLTWHEAMNRFGSDKPDLRFGQELTELTD 299 Query: 304 IVKDSDFKVFSSAIKSGGIVKGLNLKGGAGSLSRKEIDGLAEFVKPYGAKGLAW--LKVE 361 ++ ++F+VF+ AI GG V + + GGA +RKE+DG ++ K GAKGLA+ L E Sbjct: 300 YLRGTEFRVFAGAIDMGGYVGAVVMPGGA-EQTRKELDGWQDWAKARGAKGLAYVTLNAE 358 Query: 362 EGELKGPIAKFFAGETGAELQQAMGAEDGDLLFFAA--DKKEVVFDSLGALRLKLGKDFN 419 GE KGP+AK + E L +A GA+ GD +FFAA D++E + LGA RL++G+ + Sbjct: 359 TGEPKGPVAKNLSEEHLNGLAEATGAKPGDAVFFAASPDRREAQ-ELLGAARLEIGRRRD 417 Query: 420 LIDESKFNFLWVVDFPLVEYDEEAKRFVALHHPFTSPKQEDLTKLETDPASVRADAYDLV 479 LID + F W+VD P+ E ++ + A+HHPFTSP + + K E DP S YD+V Sbjct: 418 LIDLEAWAFCWIVDAPMFEPTDDG-GWSAVHHPFTSPNPDWVEKFEQDPGSALTYGYDIV 476 Query: 480 LNGYELGGGSQRIYQRPVQEKMFAALGFTEEAAQKEFGFLLEAFEYGTPPHGGIALGLDR 539 NG E+GGGS RI+ +Q ++F LG T E A ++FGFLLEAF++G PPHGGIA G DR Sbjct: 477 CNGNEIGGGSIRIHDGRLQSRVFDVLGITPEEAHEKFGFLLEAFKFGPPPHGGIAFGWDR 536 Query: 540 LVMLLAGRLNLRDTIAFPKTASASCLLTEAPGEVSLEQ 577 + LL G ++R+ IAFPKT LT AP ++ EQ Sbjct: 537 VCSLLTGSDSIREVIAFPKTGGGHDPLTGAPTPITAEQ 574 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: 934 Number of extensions: 46 Number of successful extensions: 6 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: 591 Length adjustment: 37 Effective length of query: 558 Effective length of database: 554 Effective search space: 309132 Effective search space used: 309132 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