Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_012334068.1 M446_RS20740 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B
Query= SwissProt::Q9RF06 (475 letters) >NCBI__GCF_000019365.1:WP_012334068.1 Length = 490 Score = 400 bits (1029), Expect = e-116 Identities = 215/473 (45%), Positives = 310/473 (65%), Gaps = 6/473 (1%) Query: 3 FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62 +E VIG+E+H ++ + SK+FS + FGAEPN++ +++D A PG+LPV+N+ V A+R Sbjct: 18 WEVVIGMEIHAQVTSRSKLFSGASTAFGAEPNAHVSLVDAAMPGMLPVINRECVAQAVRT 77 Query: 63 AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121 + L +I S FDRKNYFYPD P+ YQISQ+ PI G + +++ DGET R+GI RL Sbjct: 78 GLGLKAQINHRSVFDRKNYFYPDLPQGYQISQYKSPIVGEGEVLVDLPDGETIRVGIERL 137 Query: 122 HMEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179 H+E+DAGKS H SL VDLNR G L+EIVS+PD+RS +EA AY+ KLR+I++Y G Sbjct: 138 HLEQDAGKSLHDQHPSLSFVDLNRSGVALMEIVSKPDLRSSEEAKAYVTKLRTILRYLGT 197 Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239 D ME+G+LR D N+S+R G E FGT+ E+KN+NS ++ + +E E +RQ L GG Sbjct: 198 CDGDMEKGNLRADVNVSVRRPG-EPFGTRCEIKNVNSIRFIGQAIETEARRQIAILEDGG 256 Query: 240 EIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDER 299 I QETR +D + +T MR KE + DYRYFP+PD++PL I+ A+ + +R +PELPD + Sbjct: 257 WIEQETRLYDPNRNETRSMRSKEEAHDYRYFPDPDLLPLEIEQAFIDGLRTELPELPDAK 316 Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVEL 359 KA++V E GL AYDA VL + +D+FE+ + G D K +NW++ + LNK + Sbjct: 317 KARFVAEYGLSAYDATVLVAERASADYFEA-VAKGRDGKAAANWVINELFGRLNKEGHGI 375 Query: 360 LDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLL 419 + ++ L +I LI DGT+S KIAK +F + +GG+ + I+E GL Q++D + Sbjct: 376 EGSPVSAAQLGAIIDLIADGTISGKIAKDLFEIVWGEGGDPRAIVESRGLKQVTDTGAIE 435 Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472 V++ + N V K K +G+ VGQ MKA+ G+ANP VN LLK +L Sbjct: 436 AAVDQIIAANPDKVAQAK-AKPTLLGWFVGQTMKATGGKANPAAVNALLKTKL 487 Lambda K H 0.313 0.133 0.373 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: 633 Number of extensions: 27 Number of successful extensions: 6 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: 475 Length of database: 490 Length adjustment: 34 Effective length of query: 441 Effective length of database: 456 Effective search space: 201096 Effective search space used: 201096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 52 (24.6 bits)
Align candidate WP_012334068.1 M446_RS20740 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm # target sequence database: /tmp/gapView.4771.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00133 [M=481] Accession: TIGR00133 Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-163 530.5 0.0 2.1e-163 530.2 0.0 1.0 1 lcl|NCBI__GCF_000019365.1:WP_012334068.1 M446_RS20740 Asp-tRNA(Asn)/Glu-t Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019365.1:WP_012334068.1 M446_RS20740 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase GatCAB subunit B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 530.2 0.0 2.1e-163 2.1e-163 3 480 .. 17 487 .. 16 488 .. 0.97 Alignments for each domain: == domain 1 score: 530.2 bits; conditional E-value: 2.1e-163 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 ++e+viG+E+H q+ +sKlF+ +s+ + +pN +v+ v+ ++PG lPv+N+e v++A+ +l l+++ lcl|NCBI__GCF_000019365.1:WP_012334068.1 17 DWEVVIGMEIHAQVTSRSKLFSGASTAFGA-EPNAHVSLVDAAMPGMLPVINRECVAQAVRTGLGLKAQ 84 5799************************99.************************************** PP TIGR00133 72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesd 139 i+ + svFdRK+YfYpDlP+gyqi+q++ Pi+ +G++ ++l ++e ++gierlhlE+D+gks + ++ lcl|NCBI__GCF_000019365.1:WP_012334068.1 85 IN-HRSVFDRKNYFYPDLPQGYQISQYKSPIVGEGEVLVDLPDGEtIRVGIERLHLEQDAGKSLHDQH- 151 66.69************************************9988579*****************966. PP TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208 ++ s+vD+NRsgv L+EiV+kPdl+s++ea+a++ klr+ilryl+ dgd+e+G++R+DvNvs+r lcl|NCBI__GCF_000019365.1:WP_012334068.1 152 -PSLSFVDLNRSGVALMEIVSKPDLRSSEEAKAYVTKLRTILRYLGTCDGDMEKGNLRADVNVSVRRP- 218 .79***************************************************************55. PP TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277 e +gtr EiKN+ns++ i +aie E Rq+++l++g ++qetr +d +++ t s+R+Kee++DYRYf lcl|NCBI__GCF_000019365.1:WP_012334068.1 219 GEPFGTRCEIKNVNSIRFIGQAIETEARRQIAILEDGGWIEQETRLYDPNRNETRSMRSKEEAHDYRYF 287 6789***************************************************************** PP TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346 p+Pdl p+ei++ ++++ ++++lpelP+ak++r++ eygls++da vlv+++ +d+fe v+k + k lcl|NCBI__GCF_000019365.1:WP_012334068.1 288 PDPDLLPLEIEQAFIDG-LRTELPELPDAKKARFVAEYGLSAYDATVLVAERASADYFEAVAKGRDG-K 354 *****************.*****************************************99998776.* PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415 +a+nW+++el g+Lnk+ ++ + +++ +l ++i+li +g+is+k+ak+l+e + +++dp++++e + lcl|NCBI__GCF_000019365.1:WP_012334068.1 355 AAANWVINELFGRLNKEGHGIEGSPVSAAQLGAIIDLIADGTISGKIAKDLFEIVWGEGGDPRAIVESR 423 ********************************************************************* PP TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 gl q++d+ ++ ++v+++i+ np++v + k k ++l+++vGq mk t g+a+p+ v++llk +l lcl|NCBI__GCF_000019365.1:WP_012334068.1 424 GLKQVTDTGAIEAAVDQIIAANPDKVAQAK-AKPTLLGWFVGQTMKATGGKANPAAVNALLKTKL 487 **************************9876.5789**************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (490 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: 9.69 // [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