Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011813802.1 HHAL_RS05120 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000015585.1:WP_011813802.1 Length = 484 Score = 516 bits (1330), Expect = e-151 Identities = 260/477 (54%), Positives = 341/477 (71%), Gaps = 1/477 (0%) Query: 8 ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67 + E+ +H EI +L D KRI+ D ++ + + + E+ARA A D + E Sbjct: 6 VAEISAALHAGEISSRELTDSLLKRIEQFDPRLNSLITVTAEQARAAADAADARLRA-GE 64 Query: 68 HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127 G L G+P+ KD T G+ TTC S++LE F YDATVV+RL +A AV +GK NMDEF Sbjct: 65 AGPLTGVPLVHKDIFCTDGVATTCGSRMLEPFRAPYDATVVRRLAEAGAVMLGKANMDEF 124 Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187 AMGSS E S + +NPW+LD VPGGSSGGSAAAVAA P + G+DTGGSIRQPA+ G Sbjct: 125 AMGSSNETSYFGPVRNPWDLDAVPGGSSGGSAAAVAARLAPAATGTDTGGSIRQPAALSG 184 Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247 + GLKPTYGRVSRYG+VAFASSLDQ GP RT ED A LL ++G+D+ DSTS + VPD Sbjct: 185 ICGLKPTYGRVSRYGMVAFASSLDQAGPFARTAEDLALLLGGMAGLDERDSTSVDHVVPD 244 Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307 + SL I+GL+I VPKE+ GEG+ + R V AAL+VLEG GA EV LP+ + AL Sbjct: 245 YSESLNRSIRGLRIGVPKEFFGEGLDADVRSRVEAALQVLEGEGAELVEVQLPNMELALP 304 Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367 YY+++ +EAS+NLARFDG+R+G+R + +L DLYK++RAEGFG+EV+RRI++GT+ALS Sbjct: 305 AYYVIAPAEASSNLARFDGVRFGHRCADPQDLEDLYKRSRAEGFGDEVQRRILVGTYALS 364 Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427 +GYYDAYY+KAQ+VR L+ DF ++ DV+ GPT+PTPAF +GE DP+ MY +DI Sbjct: 365 AGYYDAYYRKAQQVRRLVADDFRQALDQVDVLAGPTSPTPAFDLGERADDPVQMYLSDIY 424 Query: 428 TIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPE 484 T+ VNLAG+PG+SVP G + G P+GLQ+IG +FDE+ + V H ++Q TD HK PE Sbjct: 425 TLGVNLAGLPGLSVPAGFSRGRPVGLQLIGGYFDEARLLNVGHKYQQVTDWHKQVPE 481 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: 606 Number of extensions: 20 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: 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_011813802.1 HHAL_RS05120 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A)
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.26529.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-189 615.3 0.0 4.1e-189 615.1 0.0 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011813802.1 HHAL_RS05120 Asp-tRNA(Asn)/Glu-t Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011813802.1 HHAL_RS05120 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit A # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 615.1 0.0 4.1e-189 4.1e-189 3 465 .. 11 474 .. 9 475 .. 0.99 Alignments for each domain: == domain 1 score: 615.1 bits; conditional E-value: 4.1e-189 TIGR00132 3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 ++l++ e+s++e+++++l+rie+++ ++n++++vt+e+a ++a++ d++++ e +l+g+p++ Kd + lcl|NCBI__GCF_000015585.1:WP_011813802.1 11 AALHAGEISSRELTDSLLKRIEQFDPRLNSLITVTAEQARAAADAADARLRaGEaGPLTGVPLVHKDIF 79 5788999******************************************9976646************* PP TIGR00132 70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervp 138 ++ ++ ttc+S++Le +++pydatVv+rl eaga+++Gk+N+DEFamGss etS+fg+++nP++ + vp lcl|NCBI__GCF_000015585.1:WP_011813802.1 80 CTDGVATTCGSRMLEPFRAPYDATVVRRLAEAGAVMLGKANMDEFAMGSSNETSYFGPVRNPWDLDAVP 148 ********************************************************************* PP TIGR00132 139 GGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkv 207 GGSsgGsaaavaa l+p a g+DTGgSiRqPA+++g+ GlKPtYG+vSRyG+va+asSldq G++a++ lcl|NCBI__GCF_000015585.1:WP_011813802.1 149 GGSSGGSAAAVAARLAPAATGTDTGGSIRQPAALSGICGLKPTYGRVSRYGMVAFASSLDQAGPFARTA 217 ********************************************************************* PP TIGR00132 208 edialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklleklee 276 ed+al+l ++g D++Dsts++ v+++ e+l++ ++gl++gv ke+++e+ld +v++++e++l++le lcl|NCBI__GCF_000015585.1:WP_011813802.1 218 EDLALLLGGMAGLDERDSTSVDHVVPDYSESLNRSIRGLRIGVPKEFFGEGLDADVRSRVEAALQVLEG 286 ********************************************************************* PP TIGR00132 277 lgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrR 345 +gae+vev+lp+++lal++Yy+i+p+Eassnlar+dg+r+G+r ++++l++ly+++R+egfg+ev+rR lcl|NCBI__GCF_000015585.1:WP_011813802.1 287 EGAELVEVQLPNMELALPAYYVIAPAEASSNLARFDGVRFGHRCADPQDLEDLYKRSRAEGFGDEVQRR 355 ********************************************************************* PP TIGR00132 346 imlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvl 414 i++G+yals++yyd+yy kAq+vr+l++d+f++++++vDv+++pt+pt af lge+a+dp++mylsD++ lcl|NCBI__GCF_000015585.1:WP_011813802.1 356 ILVGTYALSAGYYDAYYRKAQQVRRLVADDFRQALDQVDVLAGPTSPTPAFDLGERADDPVQMYLSDIY 424 ********************************************************************* PP TIGR00132 415 tvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465 t+ +nlaGlp++svP+g + +g p+Glq+ig +fd+ +ll+v+++++q +d lcl|NCBI__GCF_000015585.1:WP_011813802.1 425 TLGVNLAGLPGLSVPAGFS-RGRPVGLQLIGGYFDEARLLNVGHKYQQVTD 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 8.37 // [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