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_066921473.1 ACG33_RS11925 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_001579945.1:WP_066921473.1 Length = 592 Score = 749 bits (1934), Expect = 0.0 Identities = 373/588 (63%), Positives = 460/588 (78%), Gaps = 6/588 (1%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRSHYCGQ++E L GQEV++ GWVHRRRDHGGVIF+D+RDREGL Q+VFDPD E F A Sbjct: 1 MRSHYCGQVDEILSGQEVSVAGWVHRRRDHGGVIFVDLRDREGLLQIVFDPDAREIFQDA 60 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 +R+R EF V+I G VR RP G N +ASG +EVL ELE+L++AETPPF DE ++ E Sbjct: 61 ERLRGEFCVRIRGLVRPRPPGTANAALASGQVEVLARELEILSRAETPPFHHDEAAN--E 118 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 E RL+YR++DLRR M +L+LR R+T ++R YLD+ G++D+ETP+L + TPEGARDYLV Sbjct: 119 ELRLKYRYLDLRREVMQKRLRLRHRVTRAMRDYLDEQGYIDIETPMLTKATPEGARDYLV 178 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSRT+ G FFALPQSPQLFKQLLM++GFDRYYQI +CFRDEDLRA+RQPEFTQ+DIETSF Sbjct: 179 PSRTHAGQFFALPQSPQLFKQLLMMSGFDRYYQIVRCFRDEDLRAERQPEFTQLDIETSF 238 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFD-EFPHMPFEEAMRRYGSDKPDLRIPLELVDVAD 300 + E I+ E ++ +F VL E FP + + EAMRRYGSDKPDLRI LELVDVAD Sbjct: 239 MSEEQIMQHMEALICSIFATVLGDELPAPFPRITYAEAMRRYGSDKPDLRIDLELVDVAD 298 Query: 301 QLKEVEFKVFSGPANDPKGRVAALRVP-GAASMPRSQIDDYTKFVGIYGAKGLAYIKVNE 359 +++ EFKVF+ PA +P+GRVAALRVP G M R +IDD T FVG YGAKGLAY+KVNE Sbjct: 299 LVRDCEFKVFAAPAANPQGRVAALRVPQGGVRMTRKEIDDCTAFVGRYGAKGLAYVKVNE 358 Query: 360 RAKGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD 419 AKG +GLQSPI+KF+ +A + IL R A DGD++FFGAD AK+V D+LGALRIK+GHD Sbjct: 359 LAKGRDGLQSPILKFLSDAAIEGILTRAAAADGDLIFFGADTAKVVNDSLGALRIKLGHD 418 Query: 420 LKLLTREWAPMWVVDFPMFEENDDGS-LSALHHPFTSPKC-TPAELEANPGAALSRAYDM 477 L + W P+WVVDFPMFE + D ALHHPFT+P+C AEL A+P A+S+ YDM Sbjct: 419 LGMAQTGWRPLWVVDFPMFEWDADAKRWVALHHPFTAPRCEDAAELRADPANAISKGYDM 478 Query: 478 VLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAFGLD 537 VLNG+E+GGGS+RIH MQ AVF +LGI E ++KFGFLL+ALKYG PPHGG+AFGLD Sbjct: 479 VLNGSEIGGGSVRIHRPDMQSAVFDLLGIGPEEAQQKFGFLLEALKYGTPPHGGIAFGLD 538 Query: 538 RLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLR 585 R+VM M G SIR+VIAFPKTQ+A D++T AP V + L+EL+IR+R Sbjct: 539 RIVMFMAGTDSIRDVIAFPKTQTAADLLTNAPTPVSEEQLKELYIRVR 586 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: 1125 Number of extensions: 49 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: 591 Length of database: 592 Length adjustment: 37 Effective length of query: 554 Effective length of database: 555 Effective search space: 307470 Effective search space used: 307470 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 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