Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_077244138.1 B1A74_RS06550 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_001995255.1:WP_077244138.1 Length = 484 Score = 469 bits (1208), Expect = e-137 Identities = 237/469 (50%), Positives = 320/469 (68%), Gaps = 1/469 (0%) Query: 15 IHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGM 74 + +EI +L RI+ +D + +F+ + E A A D + + E L G+ Sbjct: 13 LRAREISSRELTRLYLDRIERLDADLNSFVTVTAESALEQADAADARL-AKGEEAPLLGV 71 Query: 75 PIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTE 134 P+ KD T+G+RT C S++L+ F YDATVV+R+ A AV +GK NMDEFAMGSS E Sbjct: 72 PVAQKDIFCTRGVRTACGSRMLDPFVSPYDATVVERMHAAGAVMLGKTNMDEFAMGSSNE 131 Query: 135 NSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPT 194 S Y +NPW+ VPGGSSGGSAAAV A P + G+DTGGSIRQPA+FCG+ GLKPT Sbjct: 132 TSFYGPVRNPWDTARVPGGSSGGSAAAVGARLAPGATGTDTGGSIRQPAAFCGITGLKPT 191 Query: 195 YGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTG 254 YGRVSRYG++AFASSLDQ GP+ + ED +L A++G D+ DSTS DF ++L Sbjct: 192 YGRVSRYGMIAFASSLDQGGPMAASAEDCGHMLNAMAGFDERDSTSLERPAEDFTAALDA 251 Query: 255 DIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSS 314 D+ GL+I +P+E+ GEG+ R ++ A++VL GA EVSLP+S ++ YY+++ Sbjct: 252 DLTGLRIGLPQEFFGEGLDDGIRAALDEAIRVLRERGAEIREVSLPNSHLSVPAYYVVAP 311 Query: 315 SEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAY 374 +EAS+NL+RFDG+RYGYR ++ +L+DLY ++R EGFG EVKRRIM+GT LS+GYYDAY Sbjct: 312 AEASSNLSRFDGVRYGYRCEDPQDLLDLYTRSRGEGFGAEVKRRIMVGTHVLSAGYYDAY 371 Query: 375 YKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLA 434 Y KAQKVR +I DF VF D+++GPTTP F++G + DP+ MY +DI TI NLA Sbjct: 372 YLKAQKVRRVIADDFRRVFADVDLLLGPTTPELPFELGAKSADPVKMYLSDIYTIAANLA 431 Query: 435 GVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKP 483 G+P +S+P G GLP+GLQ+IG +FDE+ + VAH F+Q TD H P Sbjct: 432 GLPAMSLPAGEVQGLPVGLQLIGNYFDEARMIGVAHQFQQETDWHARVP 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: 581 Number of extensions: 29 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_077244138.1 B1A74_RS06550 (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.17990.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-188 611.2 0.0 7.3e-188 611.0 0.0 1.0 1 lcl|NCBI__GCF_001995255.1:WP_077244138.1 B1A74_RS06550 Asp-tRNA(Asn)/Glu- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001995255.1:WP_077244138.1 B1A74_RS06550 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 ! 611.0 0.0 7.3e-188 7.3e-188 4 465 .. 12 474 .. 10 475 .. 0.99 Alignments for each domain: == domain 1 score: 611.0 bits; conditional E-value: 7.3e-188 TIGR00132 4 llkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva..kekklagipiavKdnia 70 +l ++e+s++e+++ +l+rie+ + ++n+f++vt+e+al++a++ d+++a +e +l g+p+a Kd ++ lcl|NCBI__GCF_001995255.1:WP_077244138.1 12 KLRAREISSRELTRLYLDRIERLDADLNSFVTVTAESALEQADAADARLAkgEEAPLLGVPVAQKDIFC 80 577899******************************************9974446************** PP TIGR00132 71 vkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpG 139 +++++t+c+S++L+ +vspydatVver+++aga+++GktN+DEFamGss etS++g+++nP++++rvpG lcl|NCBI__GCF_001995255.1:WP_077244138.1 81 TRGVRTACGSRMLDPFVSPYDATVVERMHAAGAVMLGKTNMDEFAMGSSNETSFYGPVRNPWDTARVPG 149 ********************************************************************* PP TIGR00132 140 GSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkve 208 GSsgGsaaav a l+p a g+DTGgSiRqPA+fcg+ GlKPtYG+vSRyG++a+asSldq G++a++ e lcl|NCBI__GCF_001995255.1:WP_077244138.1 150 GSSGGSAAAVGARLAPGATGTDTGGSIRQPAAFCGITGLKPTYGRVSRYGMIAFASSLDQGGPMAASAE 218 ********************************************************************* PP TIGR00132 209 dialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleel 277 d +l++++g D++Dstsle + e+++ +l +dl gl++g+ +e+++e+ld+++++++++++++l+e+ lcl|NCBI__GCF_001995255.1:WP_077244138.1 219 DCGHMLNAMAGFDERDSTSLERPAEDFTAALDADLTGLRIGLPQEFFGEGLDDGIRAALDEAIRVLRER 287 ********************************************************************* PP TIGR00132 278 gaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRi 346 gaei evslp+++l++++Yy+++p+Eassnl+r+dg+ryG+r e++++l +ly+++R egfg+evkrRi lcl|NCBI__GCF_001995255.1:WP_077244138.1 288 GAEIREVSLPNSHLSVPAYYVVAPAEASSNLSRFDGVRYGYRCEDPQDLLDLYTRSRGEGFGAEVKRRI 356 ********************************************************************* PP TIGR00132 347 mlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvlt 415 m+G+++ls++yyd+yy+kAqkvr++i+d+f+ +f +vD++++pt+p l+f+lg+k +dp++mylsD++t lcl|NCBI__GCF_001995255.1:WP_077244138.1 357 MVGTHVLSAGYYDAYYLKAQKVRRVIADDFRRVFADVDLLLGPTTPELPFELGAKSADPVKMYLSDIYT 425 ********************************************************************* PP TIGR00132 416 vpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465 + anlaGlpa+s+P+g+ +glp+Glq+ig++fd+ +++ va++++q++d lcl|NCBI__GCF_001995255.1:WP_077244138.1 426 IAANLAGLPAMSLPAGEV-QGLPVGLQLIGNYFDEARMIGVAHQFQQETD 474 ******************.6**************************9987 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.62 // [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