Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate Pf1N1B4_1101 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)
Query= SwissProt::O06491 (485 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 Length = 483 Score = 497 bits (1279), Expect = e-145 Identities = 247/480 (51%), Positives = 337/480 (70%), Gaps = 3/480 (0%) Query: 6 HKIT--ELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVD 63 H++T E+ + + K+ +L RI +D ++ +F++L E+ A AK D A Sbjct: 2 HQLTLAEIARGLADKKFSSEELTKVLLARIAQLDPQLNSFISLTEDLALQQAKAAD-ARR 60 Query: 64 GRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLN 123 E G L G PI KD T+G+RT+C SK+L+NF YDATVV +L A AVT+GK N Sbjct: 61 ANGESGALLGAPIAHKDLFCTQGIRTSCGSKMLDNFKAPYDATVVAKLAAAGAVTLGKTN 120 Query: 124 MDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPA 183 MDEFAMGS+ E+S Y KNPWNL+ VPGGSSGGSAAAVAA +P + G+DTGGSIRQPA Sbjct: 121 MDEFAMGSANESSYYGAVKNPWNLEHVPGGSSGGSAAAVAARLLPAATGTDTGGSIRQPA 180 Query: 184 SFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANV 243 + + GLKPTYGRVSR+G++A+ASSLDQ GP+ RT ED A LLQ ++G D DSTS + Sbjct: 181 ALTNLTGLKPTYGRVSRWGMIAYASSLDQGGPLARTAEDCAILLQGMAGFDPQDSTSIDE 240 Query: 244 DVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSK 303 VPD+ + L G ++GL+I VPKEY G+ + V+A+++ L+ LGA +E+SLP+ + Sbjct: 241 PVPDYSAGLNGSLQGLRIGVPKEYFSAGLDPRIADLVMASVEELKKLGAVVKEISLPNMQ 300 Query: 304 YALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGT 363 +A+ YY+++ +EAS+NL+RFDG+R+GYR ++ NL DLYK++R EGFG EV+RRIM+G Sbjct: 301 HAIPAYYVIAPAEASSNLSRFDGVRFGYRCEDPKNLEDLYKRSRGEGFGPEVQRRIMVGA 360 Query: 364 FALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYA 423 +ALS+GYYDAYY KAQK+R LIK DF F + D+I+GPTTP PA+K+G DP+ Y Sbjct: 361 YALSAGYYDAYYLKAQKIRRLIKNDFMAAFNEVDIILGPTTPNPAWKLGAKNSDPVAAYL 420 Query: 424 NDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483 D+ TI NLAG+PG+S+P G DGLP+G+Q++ +F E + VAH ++ TD H P Sbjct: 421 EDVYTITANLAGLPGLSMPAGFVDGLPVGVQLLAPYFQEGRLLNVAHQYQLNTDWHTRTP 480 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: 573 Number of extensions: 16 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: 483 Length adjustment: 34 Effective length of query: 451 Effective length of database: 449 Effective search space: 202499 Effective search space used: 202499 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 Pf1N1B4_1101 (Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7))
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.8283.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-181 589.1 0.0 3.5e-181 588.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 Aspartyl-tRNA(Asn) amidotransfer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl- # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 588.9 0.0 3.5e-181 3.5e-181 5 463 .. 13 472 .. 9 475 .. 0.98 Alignments for each domain: == domain 1 score: 588.9 bits; conditional E-value: 3.5e-181 TIGR00132 5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavK 66 l +k++s++e+++ +l+ri + + ++n+f+++t++ al++ak+ d++ a e l g pia K lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 13 LADKKFSSEELTKVLLARIAQLDPQLNSFISLTEDLALQQAKAADARRAnGEsGALLGAPIAHK 76 678999****************************************99875635********** PP TIGR00132 67 dniavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtkn 130 d +++++i+t+c+Sk+L+n+++pydatVv +l +aga+++GktN+DEFamGs+ e+S++g++kn lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 77 DLFCTQGIRTSCGSKMLDNFKAPYDATVVAKLAAAGAVTLGKTNMDEFAMGSANESSYYGAVKN 140 **************************************************************** PP TIGR00132 131 PeneervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvaya 194 P+n e+vpGGSsgGsaaavaa l p a g+DTGgSiRqPA++++ GlKPtYG+vSR+G++aya lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 141 PWNLEHVPGGSSGGSAAAVAARLLPAATGTDTGGSIRQPAALTNLTGLKPTYGRVSRWGMIAYA 204 **************************************************************** PP TIGR00132 195 sSldqiGilakkvedialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelsees 258 sSldq G+la++ ed a++l+ ++g D +Dsts++ +v+++ l+ l+gl++gv ke++ + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 205 SSLDQGGPLARTAEDCAILLQGMAGFDPQDSTSIDEPVPDYSAGLNGSLQGLRIGVPKEYFSAG 268 **************************************************************** PP TIGR00132 259 ldkevkekfekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrvee 322 ld ++++ + + +e+l++lga ++e+slp+++ a+++Yy+i+p+Eassnl+r+dg+r+G+r e+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 269 LDPRIADLVMASVEELKKLGAVVKEISLPNMQHAIPAYYVIAPAEASSNLSRFDGVRFGYRCED 332 **************************************************************** PP TIGR00132 323 lkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvi 386 +k+l++ly+++R egfg ev+rRim+Gayals++yyd+yy+kAqk+r+li+++f +f+evD+i lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 333 PKNLEDLYKRSRGEGFGPEVQRRIMVGAYALSAGYYDAYYLKAQKIRRLIKNDFMAAFNEVDII 396 **************************************************************** PP TIGR00132 387 vsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafdd 450 ++pt+p a klg+k++dp++ yl+Dv+t++anlaGlp++s+P+g +glp+G+q+ + +f++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 397 LGPTTPNPAWKLGAKNSDPVAAYLEDVYTITANLAGLPGLSMPAGFV-DGLPVGVQLLAPYFQE 459 ***********************************************.7*************** PP TIGR00132 451 kkllsvakaleqa 463 +ll+va++++ + lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1101 460 GRLLNVAHQYQLN 472 ********99865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (483 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 9.60 // [ok]
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