Align Aspartate--tRNA(Asp/Asn) ligase; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS; EC 6.1.1.23 (characterized)
to candidate WP_041096605.1 SUTH_RS01695 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_000828635.1:WP_041096605.1 Length = 599 Score = 748 bits (1930), Expect = 0.0 Identities = 381/595 (64%), Positives = 459/595 (77%), Gaps = 7/595 (1%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MR+HYCG++N S Q VTLCGW HRRRDHGGVIF+D+RDREGLAQVV DPDR E F A Sbjct: 1 MRTHYCGEVNASHVDQIVTLCGWNHRRRDHGGVIFIDLRDREGLAQVVCDPDRPEMFKVA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + VR+E+V+K+TGKVR RP G N N+ASG IE+L +ELEVLN A TPPF LDE ++ E Sbjct: 61 EDVRNEYVLKVTGKVRRRPAGTENSNLASGEIEILCHELEVLNAAVTPPFQLDE-ENLSE 119 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 RL +R IDLRRP+M L LR ++ + RR+LD+ GF+D+ETP+L + TPEGARDYLV Sbjct: 120 NVRLTHRVIDLRRPQMQKNLMLRYKVAMAFRRFLDEKGFIDIETPMLTKSTPEGARDYLV 179 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSR +PG FFALPQSPQLFKQLLMVAG+DRYYQI KCFRDEDLRADRQPEFTQ+DIETSF Sbjct: 180 PSRVHPGQFFALPQSPQLFKQLLMVAGYDRYYQITKCFRDEDLRADRQPEFTQVDIETSF 239 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEF-DEFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 L E I + E+M+R +FK L V+ + FP + EAMRRYGSDKPDLR+ LEL +V D Sbjct: 240 LTEEQITALMEEMIRSVFKTALAVDLPNPFPRITHAEAMRRYGSDKPDLRVTLELTEVTD 299 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNER 360 + +V FKVFSGPA GRVAALRVPG A++ R +ID YT+FV IYGA+GLAYIKVN+ Sbjct: 300 AVTDVAFKVFSGPATS-GGRVAALRVPGGAALTRGEIDGYTEFVKIYGARGLAYIKVNDA 358 Query: 361 AK-GVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD 419 +K EGLQSPIVK + EA L I++R GA GD++FFGADK KIV DALGALR K+GH+ Sbjct: 359 SKLNEEGLQSPIVKNLHEAALKTIVERTGAQSGDLIFFGADKTKIVNDALGALRTKLGHE 418 Query: 420 LKLLT-REWAPMWVVDFPMFEENDDGS-LSALHHPFTSPKCTPAELEA-NPGAALSRAYD 476 + W P+WVVDFPMFE +++ SA HHPFTSPK L A +PGA L++AYD Sbjct: 419 KGYVDGSAWRPLWVVDFPMFEYDEENKRWSACHHPFTSPKDGHEALMATDPGACLAKAYD 478 Query: 477 MVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGL 536 + LNG E+GGGS+RIH +Q+ VF+ LGI EQ+ KFGFLLDALKYGAPPHGGLAFGL Sbjct: 479 LALNGWEMGGGSVRIHRSEVQERVFQALGIGPEEQQAKFGFLLDALKYGAPPHGGLAFGL 538 Query: 537 DRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLREQPKAE 591 DR+V +M GA SIR+VIAFPKTQ A ++T AP VD K LRELHIRLR++ + + Sbjct: 539 DRIVTMMAGAESIRDVIAFPKTQRAQCLLTDAPSDVDEKQLRELHIRLRQKVETQ 593 Lambda K H 0.321 0.140 0.411 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: 1085 Number of extensions: 49 Number of successful extensions: 8 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: 591 Length of database: 599 Length adjustment: 37 Effective length of query: 554 Effective length of database: 562 Effective search space: 311348 Effective search space used: 311348 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: 53 (25.0 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