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_011032028.1 MM_RS00380 aspartate--tRNA(Asn) ligase
Query= SwissProt::Q8Q0R2 (444 letters) >NCBI__GCF_000007065.1:WP_011032028.1 Length = 444 Score = 898 bits (2320), Expect = 0.0 Identities = 444/444 (100%), Positives = 444/444 (100%) Query: 1 MSLANLRTHYTADVRPDKVENGQKVTLAGWVHEVRDLGGICFVVLRDREGKAQVTLVKKK 60 MSLANLRTHYTADVRPDKVENGQKVTLAGWVHEVRDLGGICFVVLRDREGKAQVTLVKKK Sbjct: 1 MSLANLRTHYTADVRPDKVENGQKVTLAGWVHEVRDLGGICFVVLRDREGKAQVTLVKKK 60 Query: 61 IDKDLFDAARRLVRESVISVTGSVKFEEKAPNGYELLPDEINVLNVSGSPLPMDTTGKVE 120 IDKDLFDAARRLVRESVISVTGSVKFEEKAPNGYELLPDEINVLNVSGSPLPMDTTGKVE Sbjct: 61 IDKDLFDAARRLVRESVISVTGSVKFEEKAPNGYELLPDEINVLNVSGSPLPMDTTGKVE 120 Query: 121 AELDTRLDSRFIDLRRAETTAVFKIRHESLRAIREYFVKYNFIETATPKVVATATEGGTA 180 AELDTRLDSRFIDLRRAETTAVFKIRHESLRAIREYFVKYNFIETATPKVVATATEGGTA Sbjct: 121 AELDTRLDSRFIDLRRAETTAVFKIRHESLRAIREYFVKYNFIETATPKVVATATEGGTA 180 Query: 181 LFPITYFDREAFLNQSPQLFKQILMSGGFDRVFEIGPIFRAEEHDTRRHLNEATSIDVEV 240 LFPITYFDREAFLNQSPQLFKQILMSGGFDRVFEIGPIFRAEEHDTRRHLNEATSIDVEV Sbjct: 181 LFPITYFDREAFLNQSPQLFKQILMSGGFDRVFEIGPIFRAEEHDTRRHLNEATSIDVEV 240 Query: 241 SFADHFDVMELLENLVAYVYTRVIENCKSSLEVLGVDLKVPKTPFLKLTYDEVIEIINSR 300 SFADHFDVMELLENLVAYVYTRVIENCKSSLEVLGVDLKVPKTPFLKLTYDEVIEIINSR Sbjct: 241 SFADHFDVMELLENLVAYVYTRVIENCKSSLEVLGVDLKVPKTPFLKLTYDEVIEIINSR 300 Query: 301 CEEKMHWGDDLGTLGEHTVGDHVYETTGESHYFIIDWPTEIKPFYAMPYEDRPEFSKSFD 360 CEEKMHWGDDLGTLGEHTVGDHVYETTGESHYFIIDWPTEIKPFYAMPYEDRPEFSKSFD Sbjct: 301 CEEKMHWGDDLGTLGEHTVGDHVYETTGESHYFIIDWPTEIKPFYAMPYEDRPEFSKSFD 360 Query: 361 MMHRTMELSSGAQRIHIPSLLKNRIESQGLNPDGFEFYLKAFEFGMPPHAGWGMGCERFV 420 MMHRTMELSSGAQRIHIPSLLKNRIESQGLNPDGFEFYLKAFEFGMPPHAGWGMGCERFV Sbjct: 361 MMHRTMELSSGAQRIHIPSLLKNRIESQGLNPDGFEFYLKAFEFGMPPHAGWGMGCERFV 420 Query: 421 MTMLGTENIRDTVLFPRDRRRLSP 444 MTMLGTENIRDTVLFPRDRRRLSP Sbjct: 421 MTMLGTENIRDTVLFPRDRRRLSP 444 Lambda K H 0.321 0.138 0.409 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: 826 Number of extensions: 15 Number of successful extensions: 1 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: 444 Length of database: 444 Length adjustment: 32 Effective length of query: 412 Effective length of database: 412 Effective search space: 169744 Effective search space used: 169744 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)
Align candidate WP_011032028.1 MM_RS00380 (aspartate--tRNA(Asn) ligase)
to HMM TIGR00458 (aspS: aspartate--tRNA(Asn) ligase (EC 6.1.1.23))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00458.hmm # target sequence database: /tmp/gapView.6335.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00458 [M=428] Accession: TIGR00458 Description: aspS_nondisc: aspartate--tRNA(Asn) ligase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-194 630.6 0.0 7.7e-194 630.5 0.0 1.0 1 lcl|NCBI__GCF_000007065.1:WP_011032028.1 MM_RS00380 aspartate--tRNA(Asn) Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007065.1:WP_011032028.1 MM_RS00380 aspartate--tRNA(Asn) ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 630.5 0.0 7.7e-194 7.7e-194 1 428 [] 9 444 .] 9 444 .] 0.97 Alignments for each domain: == domain 1 score: 630.5 bits; conditional E-value: 7.7e-194 TIGR00458 1 vysadikeek..dgkevllrgwvheirdlGalifvllrdregliqilvkkkkvskelfklikklkkesv 67 +y+ad+ ++k +g++v+l gwvhe+rdlG++ fv+lrdreg q+++ kkk++k+lf +++l +esv lcl|NCBI__GCF_000007065.1:WP_011032028.1 9 HYTADVRPDKveNGQKVTLAGWVHEVRDLGGICFVVLRDREGKAQVTLVKKKIDKDLFDAARRLVRESV 77 799***99864477******************************************************* PP TIGR00458 68 vavkGkvkekekapqgleiipeklevlneakeplPldleekveaeldtrldarfldlrrpkvqaifkir 136 + v+G vk +ekap+g+e++p +++vln + +plP+d + kveaeldtrld rf+dlrr+++ a+fkir lcl|NCBI__GCF_000007065.1:WP_011032028.1 78 ISVTGSVKFEEKAPNGYELLPDEINVLNVSGSPLPMDTTGKVEAELDTRLDSRFIDLRRAETTAVFKIR 146 ********************************************************************* PP TIGR00458 137 sevlesvreflaeegfievntPklvasateGGtelfeityfereaflaqsPqlykqvllaaglervyei 205 +e l+++re++ + +fie tPk+va+ateGGt lf+ityf+reafl+qsPql+kq+l++ g++rv+ei lcl|NCBI__GCF_000007065.1:WP_011032028.1 147 HESLRAIREYFVKYNFIETATPKVVATATEGGTALFPITYFDREAFLNQSPQLFKQILMSGGFDRVFEI 215 ********************************************************************* PP TIGR00458 206 aPifraeehntkrhlnevisidiemafedhkdvldileelvvrvfedvaeklkkelevlevklevpeek 274 +Pifraeeh+t+rhlne++sid+e++f+dh dv+++le+lv v++ v e++k++levl+v+l+vp+++ lcl|NCBI__GCF_000007065.1:WP_011032028.1 216 GPIFRAEEHDTRRHLNEATSIDVEVSFADHFDVMELLENLVAYVYTRVIENCKSSLEVLGVDLKVPKTP 284 ********************************************************************* PP TIGR00458 275 lerltydeaieilrakGke.ikdgedlsteaekllG.....ekmdglyfitdfPteikPfytmPdednP 337 + +ltyde iei++++ +e +++g+dl t e +G + +++yfi+d+PteikPfy+mP+ed+P lcl|NCBI__GCF_000007065.1:WP_011032028.1 285 FLKLTYDEVIEIINSRCEEkMHWGDDLGTLGEHTVGdhvyeTTGESHYFIIDWPTEIKPFYAMPYEDRP 353 **************9986549***************54442234679********************** PP TIGR00458 338 eisksfdllyrdleissGaqrihdydllvekikakGlePeslksyleafkyGmPPhaGwGlGaerlvmv 406 e+sksfd+++r++e+ssGaqrih ll+++i +Gl+P+++++yl+af++GmPPhaGwG+G er+vm+ lcl|NCBI__GCF_000007065.1:WP_011032028.1 354 EFSKSFDMMHRTMELSSGAQRIHIPSLLKNRIESQGLNPDGFEFYLKAFEFGMPPHAGWGMGCERFVMT 422 ********************************************************************* PP TIGR00458 407 lldlknireavlfPrdrkrltP 428 +l+ +nir++vlfPrdr+rl P lcl|NCBI__GCF_000007065.1:WP_011032028.1 423 MLGTENIRDTVLFPRDRRRLSP 444 ********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (428 nodes) Target sequences: 1 (444 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.51 // [ok]
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