Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_028489611.1 Q394_RS0112735 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000621325.1:WP_028489611.1 Length = 486 Score = 478 bits (1229), Expect = e-139 Identities = 227/470 (48%), Positives = 332/470 (70%), Gaps = 1/470 (0%) Query: 15 IHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGM 74 +H + + + D RI+ + ++ A++ + + A+ A ++D + G + G+ Sbjct: 13 VHTGKFSVMEATDAYLDRIERFNPELNAYITVTRDTAKTQAVDIDNRIRKGELTGAMAGV 72 Query: 75 PIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTE 134 P +KD ++G+ TTC+S +L NF YDA V ++L+ A V +GK NMDEFAMGSS E Sbjct: 73 PYALKDLFCSEGVLTTCASNMLANFISPYDAHVAEKLKAAGGVLLGKNNMDEFAMGSSNE 132 Query: 135 NSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPT 194 SA+ NPW++ VPGGSSGG AA +AA P +LG+DTGGSIRQPASFC + G+KPT Sbjct: 133 TSAFGSVCNPWDVSKVPGGSSGGGAATIAARLAPMTLGTDTGGSIRQPASFCNITGIKPT 192 Query: 195 YGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTG 254 YGR+SRYG++AFASSLDQ GP+ + ED A L I+G+D DST ++ VPD+ ++L G Sbjct: 193 YGRISRYGMIAFASSLDQCGPMAASAEDCALTLNIIAGLDGRDSTCMDLPVPDYTATLNG 252 Query: 255 DIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSS 314 ++GL+I +PKE+ EG+ + + + A+K + GA +EV+LP+S A+ YY+++ Sbjct: 253 SLEGLRIGLPKEFFAEGLDAQVADVIDRAIKQFQAKGAIIKEVTLPNSHLAVPVYYVVAP 312 Query: 315 SEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAY 374 +E S+NL+RFDG+R+G+R +N +L+DLY+++R EGFG+EVKRRIM+GT+ALS+GYYDAY Sbjct: 313 AECSSNLSRFDGVRFGHRCENPKDLMDLYERSRWEGFGDEVKRRIMIGTYALSAGYYDAY 372 Query: 375 YKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLA 434 Y KAQ+VR LIK+DFE F+ DVI+GP+ PT AF IGE DP++MY D+ TIPV+LA Sbjct: 373 YLKAQQVRRLIKQDFEAAFKDVDVIMGPSCPTTAFGIGEKKDDPISMYLEDLYTIPVSLA 432 Query: 435 GVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483 G+PG++ P G ADGLP+G+Q++G +F+E+ + +AH ++Q TD H P Sbjct: 433 GLPGMTFPIGFAADGLPVGMQLVGNYFEEARMLNIAHQYQQWTDWHTQVP 482 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: 599 Number of extensions: 26 Number of successful extensions: 2 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: 486 Length adjustment: 34 Effective length of query: 451 Effective length of database: 452 Effective search space: 203852 Effective search space used: 203852 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_028489611.1 Q394_RS0112735 (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.21341.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-186 604.8 0.0 6e-186 604.6 0.0 1.0 1 lcl|NCBI__GCF_000621325.1:WP_028489611.1 Q394_RS0112735 Asp-tRNA(Asn)/Glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000621325.1:WP_028489611.1 Q394_RS0112735 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 ! 604.6 0.0 6e-186 6e-186 4 465 .. 12 476 .. 9 477 .. 0.98 Alignments for each domain: == domain 1 score: 604.6 bits; conditional E-value: 6e-186 TIGR00132 4 llkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.k.klagipiavKdni 69 +++ ++s+ e+++++l+rie+++ ++na+++vt+++a ++a +d++++ e + +ag+p+a+Kd + lcl|NCBI__GCF_000621325.1:WP_028489611.1 12 GVHTGKFSVMEATDAYLDRIERFNPELNAYITVTRDTAKTQAVDIDNRIRkGElTgAMAGVPYALKDLF 80 577889999****************************************97445569************ PP TIGR00132 70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervp 138 + +++ ttcaS++L n++spyda+V e+lk+ag +++Gk N+DEFamGss etSafg + nP++ ++vp lcl|NCBI__GCF_000621325.1:WP_028489611.1 81 CSEGVLTTCASNMLANFISPYDAHVAEKLKAAGGVLLGKNNMDEFAMGSSNETSAFGSVCNPWDVSKVP 149 ********************************************************************* PP TIGR00132 139 GGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkv 207 GGSsgG aa++aa l+p++lg+DTGgSiRqPAsfc++ G+KPtYG++SRyG++a+asSldq G++a++ lcl|NCBI__GCF_000621325.1:WP_028489611.1 150 GGSSGGGAATIAARLAPMTLGTDTGGSIRQPASFCNITGIKPTYGRISRYGMIAFASSLDQCGPMAASA 218 ********************************************************************* PP TIGR00132 208 edialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklleklee 276 ed al l++i+g D +Dst ++ +v++++ +l+ l gl++g+ ke++ e+ld +v++ ++++++++++ lcl|NCBI__GCF_000621325.1:WP_028489611.1 219 EDCALTLNIIAGLDGRDSTCMDLPVPDYTATLNGSLEGLRIGLPKEFFAEGLDAQVADVIDRAIKQFQA 287 ********************************************************************* PP TIGR00132 277 lgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrR 345 +ga i+ev lp+++la+++Yy+++p+E ssnl+r+dg+r+G+r e++k+l++ly ++R egfg+evkrR lcl|NCBI__GCF_000621325.1:WP_028489611.1 288 KGAIIKEVTLPNSHLAVPVYYVVAPAECSSNLSRFDGVRFGHRCENPKDLMDLYERSRWEGFGDEVKRR 356 ********************************************************************* PP TIGR00132 346 imlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvl 414 im+G+yals++yyd+yy+kAq+vr+li+++fe +f++vDvi++p+ pt+af +gek++dp++myl+D++ lcl|NCBI__GCF_000621325.1:WP_028489611.1 357 IMIGTYALSAGYYDAYYLKAQQVRRLIKQDFEAAFKDVDVIMGPSCPTTAFGIGEKKDDPISMYLEDLY 425 ********************************************************************* PP TIGR00132 415 tvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465 t+p++laGlp+++ P+g + +glp+G+q++g++f++ ++l++a++++q +d lcl|NCBI__GCF_000621325.1:WP_028489611.1 426 TIPVSLAGLPGMTFPIGFAADGLPVGMQLVGNYFEEARMLNIAHQYQQWTD 476 **********************************************99765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (486 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: 11.20 // [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