Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_006746095.1 THITH_RS02415 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000227685.2:WP_006746095.1 Length = 484 Score = 499 bits (1284), Expect = e-145 Identities = 251/469 (53%), Positives = 329/469 (70%), Gaps = 1/469 (0%) Query: 15 IHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGM 74 + ++I +L + +R+ +D ++ +F+ + E A A A D + + E +L G+ Sbjct: 13 LRARDISSRELTELYLERVDRLDAQINSFVTVTPEAALAAADAADRRL-AKGEQAVLLGV 71 Query: 75 PIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTE 134 P+ KD T+G+RT+C SK+L+ F YDATVV+R+ A AVT+GK NMDEFAMGSS E Sbjct: 72 PVAQKDIFCTRGVRTSCGSKMLDPFVAPYDATVVERMNAAGAVTLGKTNMDEFAMGSSNE 131 Query: 135 NSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPT 194 S Y +NPW+ D VPGGSSGGSAAAVAA VP + G+DTGGSIRQPA+FCG+ G+KPT Sbjct: 132 TSFYGPVRNPWDADRVPGGSSGGSAAAVAARLVPAATGTDTGGSIRQPAAFCGITGVKPT 191 Query: 195 YGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTG 254 YGRVSRYG++AFASSLDQ GP+ T ED A +L A++G D DSTS DF + L Sbjct: 192 YGRVSRYGMIAFASSLDQGGPMAATAEDCALMLNAMAGFDPRDSTSVERPDEDFTAGLKA 251 Query: 255 DIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSS 314 ++KGL+I +PKE+ G+G+ RE AAL VL+ GA E+SLP+S ++ YY+++ Sbjct: 252 NLKGLRIGLPKEFFGDGLDSSVREVTEAALAVLKDRGAELVEISLPNSGLSVPAYYVVAP 311 Query: 315 SEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAY 374 +E S+NLAR+DG+RYGYR +L DLY +TRAEGFG EVKRRIM+GT+ LS+GYYDAY Sbjct: 312 AECSSNLARYDGVRYGYRCAEPRDLTDLYTRTRAEGFGAEVKRRIMIGTYVLSAGYYDAY 371 Query: 375 YKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLA 434 Y KAQKVR LI DF FE+ DVI GPTTP F++GE + DP+ MY +DI TI VNLA Sbjct: 372 YLKAQKVRRLIADDFRRAFEQVDVIAGPTTPELPFRLGEKSADPVKMYLSDIYTIAVNLA 431 Query: 435 GVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483 G+PG+S+P G LP+GLQ+IG +FDES + VAH F+Q TD H P Sbjct: 432 GLPGLSMPAGTVGCLPVGLQLIGNYFDESRLLGVAHQFQQDTDWHARMP 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: 566 Number of extensions: 17 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_006746095.1 THITH_RS02415 (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.8862.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-192 625.5 0.0 3.4e-192 625.2 0.0 1.0 1 lcl|NCBI__GCF_000227685.2:WP_006746095.1 THITH_RS02415 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000227685.2:WP_006746095.1 THITH_RS02415 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 ! 625.2 0.0 3.4e-192 3.4e-192 5 465 .. 13 474 .. 10 475 .. 0.98 Alignments for each domain: == domain 1 score: 625.2 bits; conditional E-value: 3.4e-192 TIGR00132 5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniav 71 l ++++s++e++e +ler+++ + +in+f++vt+e al++a++ d+++a e l g+p+a Kd +++ lcl|NCBI__GCF_000227685.2:WP_006746095.1 13 LRARDISSRELTELYLERVDRLDAQINSFVTVTPEAALAAADAADRRLAkGEqAVLLGVPVAQKDIFCT 81 6678999****************************************9974426*************** PP TIGR00132 72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGG 140 ++++t+c+Sk+L+ +v+pydatVver+++aga+++GktN+DEFamGss etS++g+++nP++ +rvpGG lcl|NCBI__GCF_000227685.2:WP_006746095.1 82 RGVRTSCGSKMLDPFVAPYDATVVERMNAAGAVTLGKTNMDEFAMGSSNETSFYGPVRNPWDADRVPGG 150 ********************************************************************* PP TIGR00132 141 SsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkved 209 SsgGsaaavaa lvp a g+DTGgSiRqPA+fcg+ G+KPtYG+vSRyG++a+asSldq G++a++ ed lcl|NCBI__GCF_000227685.2:WP_006746095.1 151 SSGGSAAAVAARLVPAATGTDTGGSIRQPAAFCGITGVKPTYGRVSRYGMIAFASSLDQGGPMAATAED 219 ********************************************************************* PP TIGR00132 210 ialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelg 278 al+l++++g D +Dsts+e ++e+++ lk++lkgl++g+ ke+++++ld++v+e e++l +l+++g lcl|NCBI__GCF_000227685.2:WP_006746095.1 220 CALMLNAMAGFDPRDSTSVERPDEDFTAGLKANLKGLRIGLPKEFFGDGLDSSVREVTEAALAVLKDRG 288 ********************************************************************* PP TIGR00132 279 aeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRim 347 ae+ve+slp++ l++++Yy+++p+E ssnlarydg+ryG+r e+++l++ly++tR+egfg+evkrRim lcl|NCBI__GCF_000227685.2:WP_006746095.1 289 AELVEISLPNSGLSVPAYYVVAPAECSSNLARYDGVRYGYRCAEPRDLTDLYTRTRAEGFGAEVKRRIM 357 ********************************************************************* PP TIGR00132 348 lGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltv 416 +G+y+ls++yyd+yy+kAqkvr+li+d+f+ +fe+vDvi++pt+p l+f+lgek +dp++mylsD++t+ lcl|NCBI__GCF_000227685.2:WP_006746095.1 358 IGTYVLSAGYYDAYYLKAQKVRRLIADDFRRAFEQVDVIAGPTTPELPFRLGEKSADPVKMYLSDIYTI 426 ********************************************************************* PP TIGR00132 417 panlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465 +nlaGlp++s+P+g+ lp+Glq+ig++fd+++ll va++++q +d lcl|NCBI__GCF_000227685.2:WP_006746095.1 427 AVNLAGLPGLSMPAGTV-GCLPVGLQLIGNYFDESRLLGVAHQFQQDTD 474 *****************.59*************************9876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9.74 // [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