Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_085219215.1 B9N75_RS13220 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_900177405.1:WP_085219215.1 Length = 497 Score = 437 bits (1123), Expect = e-127 Identities = 235/471 (49%), Positives = 312/471 (66%), Gaps = 14/471 (2%) Query: 26 VDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSEHGLLFGMPIGVKDNIVTK 85 V E+Y A + AF+ + A A A + D G + L G+PIG+KD TK Sbjct: 26 VAEAYNAAVAGAKALNAFVIETPDHALAAADQADRDRAGGTLKPLS-GVPIGMKDLFATK 84 Query: 86 GLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEFAMGSSTENSAYKLTKNPW 145 G++TT S +LE F P+Y++TV QRL DA A +GKLNMD+FAMGSS E S + +PW Sbjct: 85 GVQTTAGSHMLEGFTPVYESTVSQRLWDAGAGMLGKLNMDQFAMGSSNETSYFGNVISPW 144 Query: 146 ------NLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCGVVGLKPTYGRVS 199 N PGGSSGGS+AAVAA P + G+DTGGSIRQPA+F G+ G+KPTYGR S Sbjct: 145 RRGDGGNAPLAPGGSSGGSSAAVAARLCPGATGTDTGGSIRQPAAFTGISGIKPTYGRCS 204 Query: 200 RYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPDFLSSLTGDIKGL 259 R+G+VAF+SSLDQ GP+ R V D A LL+A+SG D DSTS +DVP + ++L+ D++G Sbjct: 205 RWGIVAFSSSLDQAGPMARDVRDCAILLEAMSGFDPKDSTSLQMDVPAWDANLSADLRGK 264 Query: 260 KIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALATYYLLSSSEASA 319 K+ +PKEY +G+ E + + + GA E+SLPH+KYAL TYY+++ +EAS+ Sbjct: 265 KVGIPKEYRIDGIPAEIDRAWEQGIAWAKDAGAEIVEISLPHTKYALPTYYIIAPAEASS 324 Query: 320 NLARFDGIRYGYR-----TDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALSSGYYDAY 374 NLAR+DG+RYG R + L ++YK TRA GFG EVKRRIM+GT+ LS+G+YDAY Sbjct: 325 NLARYDGVRYGQRVAGEGSGTGAGLAEMYKATRAAGFGAEVKRRIMIGTYVLSAGFYDAY 384 Query: 375 YKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDILTIPVNLA 434 + +AQKVR LI +DF+ FE DVI+ PT P+ +F +GE + DP+ MY ND+ +P +LA Sbjct: 385 FNQAQKVRALIARDFQKAFETVDVILTPTAPSASFALGEKSADPIAMYLNDVFAVPASLA 444 Query: 435 GVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPE 484 G+P +SVP L D GLPLGLQIIG+ FDE V A E A+PE Sbjct: 445 GLPAMSVPAALDDQGLPLGLQIIGRAFDEQGVLNAGLAIEHRAG-FTARPE 494 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: 621 Number of extensions: 30 Number of successful extensions: 4 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: 497 Length adjustment: 34 Effective length of query: 451 Effective length of database: 463 Effective search space: 208813 Effective search space used: 208813 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_085219215.1 B9N75_RS13220 (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.1117858.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-169 550.2 0.0 2.2e-169 550.0 0.0 1.0 1 NCBI__GCF_900177405.1:WP_085219215.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085219215.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 550.0 0.0 2.2e-169 2.2e-169 5 463 .. 16 486 .. 12 489 .. 0.96 Alignments for each domain: == domain 1 score: 550.0 bits; conditional E-value: 2.2e-169 TIGR00132 5 lkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavkdie 75 +k+ +s++ev+e++++++ k +naf+ t+++al++a++ d++ a + k+l g+pi++Kd +a+k+++ NCBI__GCF_900177405.1:WP_085219215.1 16 VKDGAFSAREVAEAYNAAVAGAKA-LNAFVIETPDHALAAADQADRDRAgGTlKPLSGVPIGMKDLFATKGVQ 87 667778889999999999988888.*********************99975558******************* PP TIGR00132 76 ttcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPe......neervpGGSs 142 tt++S++Le+++++y++tV +rl +aga ++Gk N+D FamGss etS+fg + P+ n pGGSs NCBI__GCF_900177405.1:WP_085219215.1 88 TTAGSHMLEGFTPVYESTVSQRLWDAGAGMLGKLNMDQFAMGSSNETSYFGNVISPWrrgdggNAPLAPGGSS 160 ********************************************************633333366789***** PP TIGR00132 143 gGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvld 215 gGs+aavaa l+p a g+DTGgSiRqPA+f+g+ G+KPtYG+ SR+G+va++sSldq G++a++v d a++l+ NCBI__GCF_900177405.1:WP_085219215.1 161 GGSSAAVAARLCPGATGTDTGGSIRQPAAFTGISGIKPTYGRCSRWGIVAFSSSLDQAGPMARDVRDCAILLE 233 ************************************************************************* PP TIGR00132 216 visgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslps 288 ++sg D kDstsl+++v+ + +l +dl+g kvg+ ke++ ++++ e+++++e+ + ++ gaeive+slp+ NCBI__GCF_900177405.1:WP_085219215.1 234 AMSGFDPKDSTSLQMDVPAWDANLSADLRGKKVGIPKEYRIDGIPAEIDRAWEQGIAWAKDAGAEIVEISLPH 306 ************************************************************************* PP TIGR00132 289 vklalaiYyiispsEassnlarydgiryGkrveelks.....lkelyaktRsegfgeevkrRimlGayalske 356 k+al++Yyii+p+Eassnlarydg+ryG+rv s l e+y++tR++gfg+evkrRim+G+y+ls++ NCBI__GCF_900177405.1:WP_085219215.1 307 TKYALPTYYIIAPAEASSNLARYDGVRYGQRVAGEGSgtgagLAEMYKATRAAGFGAEVKRRIMIGTYVLSAG 379 ********************************9998889999******************************* PP TIGR00132 357 yydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpaisvP 429 yd+y+++Aqkvr li+++f+k+fe vDvi++ptap +f lgek +dp++myl+Dv+ vpa+laGlpa+svP NCBI__GCF_900177405.1:WP_085219215.1 380 FYDAYFNQAQKVRALIARDFQKAFETVDVILTPTAPSASFALGEKSADPIAMYLNDVFAVPASLAGLPAMSVP 452 ************************************************************************* PP TIGR00132 430 lgkkekglpiGlqiigkafddkkllsvakaleqa 463 ++ +++glp+Glqiig+afd++ +l+++ a+e++ NCBI__GCF_900177405.1:WP_085219215.1 453 AALDDQGLPLGLQIIGRAFDEQGVLNAGLAIEHR 486 ***************************9999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (497 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: 00:00:00.01 # Mc/sec: 17.99 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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