Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate Dsui_0886 Dsui_0886 glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, A subunit
Query= SwissProt::O06491 (485 letters) >FitnessBrowser__PS:Dsui_0886 Length = 489 Score = 476 bits (1226), Expect = e-139 Identities = 241/486 (49%), Positives = 328/486 (67%), Gaps = 6/486 (1%) Query: 3 LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62 + + + EL Q + K+I +L RI ++ + A+++ ER+ A AK D + Sbjct: 1 MLNSSLKELAQALAGKKISSVELTQLYLDRINRLNPAINAYVSTQPERSLAQAKAADARL 60 Query: 63 DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122 + G L G+P+ KD +G TTC SK+L NF YDATV+Q+ A AV +GK Sbjct: 61 -AAGDAGPLTGIPLAQKDIFCAEGWLTTCGSKMLANFVSPYDATVIQKFDAAGAVNLGKT 119 Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182 NMDEFAMGSS E S + KNPW+ VPGGSSGGSAAAVAA P + G+DTGGSIRQP Sbjct: 120 NMDEFAMGSSNETSFFGPVKNPWDQSRVPGGSSGGSAAAVAARLAPAATGTDTGGSIRQP 179 Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242 A+ C + GLKPTYG VSR+G++AFASSLDQ GP+ R+ ED LL A++G D DSTS Sbjct: 180 AALCNLTGLKPTYGVVSRWGMIAFASSLDQAGPMARSAEDCGLLLNAMAGFDPKDSTSLE 239 Query: 243 VDVPDFLSSLTGD-----IKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEV 297 V D+ L + GLK+ +PKE+ GEG ++ AA++ + LGA EV Sbjct: 240 RPVEDYTRELNAPASAKPLAGLKVGLPKEFFGEGCDAAVMAAIQAAIEQYKALGAEMVEV 299 Query: 298 SLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKR 357 SLP+ K ++ YY+++ +EAS+NL+RFDG+RYGYR D+L D+Y ++RA+GFG EVKR Sbjct: 300 SLPNMKLSVPAYYVIAPAEASSNLSRFDGVRYGYRASEYDSLDDMYAKSRAQGFGAEVKR 359 Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKD 417 RI++GT+ LS GYYDAYY +AQ++R LI +DF F++ DVI+GPT+P+ AFK+G+ D Sbjct: 360 RILIGTYVLSHGYYDAYYLQAQRIRRLIAEDFVAAFKQCDVILGPTSPSTAFKLGDKAGD 419 Query: 418 PLTMYANDILTIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATD 477 P+ MY +DI TI VNLAG+PG+S+PCG A+GLP+GLQ+IG +FDE+ + VAH ++Q TD Sbjct: 420 PVQMYLSDIYTIAVNLAGLPGMSLPCGFAEGLPVGLQLIGNYFDEARLLNVAHRYQQVTD 479 Query: 478 HHKAKP 483 H P Sbjct: 480 WHGRAP 485 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: 585 Number of extensions: 18 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: 489 Length adjustment: 34 Effective length of query: 451 Effective length of database: 455 Effective search space: 205205 Effective search space used: 205205 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 Dsui_0886 Dsui_0886 (glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, A subunit)
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.16203.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-190 619.0 0.0 2.9e-190 618.8 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_0886 Dsui_0886 glutamyl-tRNA(Gln) and Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_0886 Dsui_0886 glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, A subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 618.8 0.0 2.9e-190 2.9e-190 2 465 .. 10 479 .. 9 480 .. 0.98 Alignments for each domain: == domain 1 score: 618.8 bits; conditional E-value: 2.9e-190 TIGR00132 2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdiet 76 +++l k++s++e+++ +l+ri++ + ina++++++e++l++ak+ d+++a + +l+gip+a Kd ++ +++ t lcl|FitnessBrowser__PS:Dsui_0886 10 AQALAGKKISSVELTQLYLDRINRLNPAINAYVSTQPERSLAQAKAADARLAaGDaGPLTGIPLAQKDIFCAEGWLT 86 5788899*******************************************9975536******************** PP TIGR00132 77 tcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGsaaavaadl 153 tc+Sk+L n+vspydatV+++ +aga+ +GktN+DEFamGss etS+fg++knP++++rvpGGSsgGsaaavaa l lcl|FitnessBrowser__PS:Dsui_0886 87 TCGSKMLANFVSPYDATVIQKFDAAGAVNLGKTNMDEFAMGSSNETSFFGPVKNPWDQSRVPGGSSGGSAAAVAARL 163 ***************************************************************************** PP TIGR00132 154 vplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkDkkDstslev 230 +p a g+DTGgSiRqPA++c+ GlKPtYG+vSR+G++a+asSldq G++a++ ed l+l++++g D kDstsle lcl|FitnessBrowser__PS:Dsui_0886 164 APAATGTDTGGSIRQPAALCNLTGLKPTYGVVSRWGMIAFASSLDQAGPMARSAEDCGLLLNAMAGFDPKDSTSLER 240 ***************************************************************************** PP TIGR00132 231 kveelleelkk.....dlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiisps 302 +ve++++el++ l glkvg+ ke+++e++d +v++++++++e+ ++lgae+vevslp++kl++++Yy+i+p+ lcl|FitnessBrowser__PS:Dsui_0886 241 PVEDYTRELNApasakPLAGLKVGLPKEFFGEGCDAAVMAAIQAAIEQYKALGAEMVEVSLPNMKLSVPAYYVIAPA 317 *******99887755557799******************************************************** PP TIGR00132 303 EassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykkAqkvrtliidefekl 379 Eassnl+r+dg+ryG+r++e++sl+++yak+R++gfg+evkrRi++G+y+ls++yyd+yy++Aq++r+li+++f + lcl|FitnessBrowser__PS:Dsui_0886 318 EASSNLSRFDGVRYGYRASEYDSLDDMYAKSRAQGFGAEVKRRILIGTYVLSHGYYDAYYLQAQRIRRLIAEDFVAA 394 ***************************************************************************** PP TIGR00132 380 feevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsv 456 f+++Dvi++pt+p +afklg+ka dp++mylsD++t+ +nlaGlp++s+P+g + +glp+Glq+ig++fd+ +ll+v lcl|FitnessBrowser__PS:Dsui_0886 395 FKQCDVILGPTSPSTAFKLGDKAGDPVQMYLSDIYTIAVNLAGLPGMSLPCGFA-EGLPVGLQLIGNYFDEARLLNV 470 ******************************************************.7********************* PP TIGR00132 457 akaleqald 465 a+ ++q +d lcl|FitnessBrowser__PS:Dsui_0886 471 AHRYQQVTD 479 ****99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (489 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: 9.11 // [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