Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_019894380.1 A377_RS0101715 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000384235.1:WP_019894380.1 Length = 484 Score = 477 bits (1227), Expect = e-139 Identities = 237/471 (50%), Positives = 329/471 (69%), Gaps = 1/471 (0%) Query: 11 LKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGL 70 L + + +E+ L RI D ++ AF+ + E A A+ D +D R E Sbjct: 9 LSERLQSRELTSVALTQHFLDRIARFDGELNAFVTVTPELALEMAQAADAKLD-RGEGHR 67 Query: 71 LFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMG 130 L G+P+ KD T ++T+C SK+L NF YDA VV++L+ + +GK NMDEFAMG Sbjct: 68 LTGIPVAHKDIFCTLDVKTSCGSKMLNNFLSPYDAAVVEKLKSLDMPMLGKTNMDEFAMG 127 Query: 131 SSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVG 190 SSTE+S Y T NPW+ VPGGSSGGSAAAVAAG P + GSDTGGSIRQPA+FCG+ G Sbjct: 128 SSTESSYYGRTLNPWDHRAVPGGSSGGSAAAVAAGLAPVATGSDTGGSIRQPAAFCGISG 187 Query: 191 LKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLS 250 +KPTYG VSRYG++A+ASS DQ GP+ R+ ED A+LL+A++G+D+ DSTS + D+ Sbjct: 188 IKPTYGAVSRYGMIAYASSFDQGGPMARSAEDAAWLLEAMAGLDERDSTSVALASTDYSR 247 Query: 251 SLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYY 310 L+ ++G+K+ VP+EY EG+ + E+V A+ LE LGA + LP+ A+++YY Sbjct: 248 DLSRSVQGMKVGVPEEYFSEGLEADVAETVQQAIGELEKLGAEIVRIHLPNKDLAVSSYY 307 Query: 311 LLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGY 370 +L+ +EAS+NL+RFDG+RYG+R + +L DLY ++R+EGFG+EVKRRIM+GT+ LS GY Sbjct: 308 VLAPAEASSNLSRFDGVRYGHRCEAPKDLNDLYTRSRSEGFGDEVKRRIMVGTYVLSEGY 367 Query: 371 YDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIP 430 YDAYY+KAQK+R L++ DF FE+ D+IVGP P+ AF IGE T DP++MY D+ TIP Sbjct: 368 YDAYYRKAQKLRRLVRDDFVKAFEQCDLIVGPVAPSVAFDIGEKTDDPVSMYLADLYTIP 427 Query: 431 VNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKA 481 VNLAG+P +S+P G A G P+GL I+G +F+E + ++AH ++Q TD H A Sbjct: 428 VNLAGLPAMSIPAGFARGRPVGLHIVGPYFEEHKILQLAHQYQQVTDWHHA 478 Lambda K H 0.315 0.134 0.381 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: 568 Number of extensions: 19 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: 485 Length of database: 484 Length adjustment: 34 Effective length of query: 451 Effective length of database: 450 Effective search space: 202950 Effective search space used: 202950 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
Align candidate WP_019894380.1 A377_RS0101715 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (EC 6.3.5.-))
# 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/TIGR00132.hmm # target sequence database: /tmp/gapView.15997.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00132 [M=466] Accession: TIGR00132 Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-190 618.0 0.0 6.1e-190 617.8 0.0 1.0 1 lcl|NCBI__GCF_000384235.1:WP_019894380.1 A377_RS0101715 Asp-tRNA(Asn)/Glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_019894380.1 A377_RS0101715 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 617.8 0.0 6.1e-190 6.1e-190 3 465 .. 11 474 .. 9 475 .. 0.99 Alignments for each domain: == domain 1 score: 617.8 bits; conditional E-value: 6.1e-190 TIGR00132 3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 e l+++e++++++++++l+ri +++ ++naf++vt+e al++a++ d+k++ e ++l+gip+a Kd + lcl|NCBI__GCF_000384235.1:WP_019894380.1 11 ERLQSRELTSVALTQHFLDRIARFDGELNAFVTVTPELALEMAQAADAKLDrGEgHRLTGIPVAHKDIF 79 678899********************************************976656************* PP TIGR00132 70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervp 138 ++ d++t+c+Sk+L+n+ spyda Vve+lk+ ++ ++GktN+DEFamGsste+S++g t nP++++ vp lcl|NCBI__GCF_000384235.1:WP_019894380.1 80 CTLDVKTSCGSKMLNNFLSPYDAAVVEKLKSLDMPMLGKTNMDEFAMGSSTESSYYGRTLNPWDHRAVP 148 ********************************************************************* PP TIGR00132 139 GGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkv 207 GGSsgGsaaavaa+l+p+a gsDTGgSiRqPA+fcg+ G+KPtYG+vSRyG++ayasS+dq G++a++ lcl|NCBI__GCF_000384235.1:WP_019894380.1 149 GGSSGGSAAAVAAGLAPVATGSDTGGSIRQPAAFCGISGIKPTYGAVSRYGMIAYASSFDQGGPMARSA 217 ********************************************************************* PP TIGR00132 208 edialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklleklee 276 ed+a +l++++g D++Dsts+ + +++ ++l + ++g+kvgv +e++ e+l+ +v+e++++++ +le+ lcl|NCBI__GCF_000384235.1:WP_019894380.1 218 EDAAWLLEAMAGLDERDSTSVALASTDYSRDLSRSVQGMKVGVPEEYFSEGLEADVAETVQQAIGELEK 286 ********************************************************************* PP TIGR00132 277 lgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrR 345 lgaeiv ++lp+ +la++ Yy+++p+Eassnl+r+dg+ryG+r e +k+l++ly+++Rsegfg+evkrR lcl|NCBI__GCF_000384235.1:WP_019894380.1 287 LGAEIVRIHLPNKDLAVSSYYVLAPAEASSNLSRFDGVRYGHRCEAPKDLNDLYTRSRSEGFGDEVKRR 355 ********************************************************************* PP TIGR00132 346 imlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvl 414 im+G+y+ls++yyd+yy kAqk+r+l++d+f k+fe++D+iv+p+ap +af +gek++dp++myl+D++ lcl|NCBI__GCF_000384235.1:WP_019894380.1 356 IMVGTYVLSEGYYDAYYRKAQKLRRLVRDDFVKAFEQCDLIVGPVAPSVAFDIGEKTDDPVSMYLADLY 424 ********************************************************************* PP TIGR00132 415 tvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465 t+p+nlaGlpa+s+P+g + +g p+Gl i+g +f+++k+l++a++++q +d lcl|NCBI__GCF_000384235.1:WP_019894380.1 425 TIPVNLAGLPAMSIPAGFA-RGRPVGLHIVGPYFEEHKILQLAHQYQQVTD 474 *******************.7*************************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (484 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9.20 // [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