Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_068169806.1 HTA01S_RS09255 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
Query= SwissProt::Q9RF06 (475 letters) >NCBI__GCF_001592305.1:WP_068169806.1 Length = 506 Score = 406 bits (1043), Expect = e-117 Identities = 215/491 (43%), Positives = 309/491 (62%), Gaps = 22/491 (4%) Query: 3 FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62 +E VIG E H +L T SK+FS +P FGAEPN+ +DLA PG LPV+N+ AV+ A+R Sbjct: 16 YEVVIGFETHAQLATQSKIFSRAPTAFGAEPNTQACAVDLALPGTLPVMNRGAVEHAIRL 75 Query: 63 AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITRLH 122 +AL IA +S F RKNYFYPD PK YQISQF+ P+ + G + + E K + + R H Sbjct: 76 GLALGSHIAEQSVFARKNYFYPDLPKGYQISQFEIPVVQGGEVSFFLGDEKKTVRLVRAH 135 Query: 123 MEEDAGKSTHKGEYSL--VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVS 180 +EEDAGKS H+ + + +DLNR GTPL+EIV+EPD+RS EA AY ++L I+ + GV Sbjct: 136 LEEDAGKSLHEEFHGMSGIDLNRAGTPLLEIVTEPDMRSSAEAVAYAKELHKIVTWIGVC 195 Query: 181 DVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGGE 240 D M+EGS RCDAN+S+R G + GT+ E+KNLNSF ++++ ++YE + Q E++ G Sbjct: 196 DGNMQEGSFRCDANVSVRKPG-DPLGTRREIKNLNSFKFMQQAIDYEVRWQIEQIEDGHA 254 Query: 241 IGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDERK 300 I Q T FD TG+T MR KE + DYRYFP+PD+ PL I W E+V+ +PELP + Sbjct: 255 IQQATVLFDPDTGETRAMRTKEDAADYRYFPDPDLPPLVIARDWVEQVKAGMPELPRQMA 314 Query: 301 AKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVELL 360 ++V + LP YDA LT + M+ +FE+ + KL SNW+MG ++ LN ++ + Sbjct: 315 ERFVRDYALPEYDATTLTQSPAMAAYFETAAKACGQPKLVSNWIMGEMSRRLNAGEIGID 374 Query: 361 DTKLTPENLAGMIKLIEDGTMSSKIAKKVFPEL---AAKGGNAK---------------- 401 ++P+ L +I I GT+++ AK++F L A+ G A Sbjct: 375 HAPVSPKQLGEIITNIVSGTINNGGAKQLFDHLWQHPAQVGQASSLDPVTQFGNPTTSVA 434 Query: 402 QIMEDNGLVQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANP 461 ++++ GL Q++D L K ++E + N +V ++ GK KA LVGQ+MKASKG+ANP Sbjct: 435 EMIDSLGLKQMNDAGALEKIIDEVMAANADNVAQFRAGKDKAFNALVGQVMKASKGKANP 494 Query: 462 QLVNQLLKQEL 472 Q VN LL+Q+L Sbjct: 495 QQVNDLLRQKL 505 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: 581 Number of extensions: 26 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: 475 Length of database: 506 Length adjustment: 34 Effective length of query: 441 Effective length of database: 472 Effective search space: 208152 Effective search space used: 208152 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_068169806.1 HTA01S_RS09255 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
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.991.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-164 533.5 0.0 2.4e-164 533.3 0.0 1.0 1 lcl|NCBI__GCF_001592305.1:WP_068169806.1 HTA01S_RS09255 Asp-tRNA(Asn)/Glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001592305.1:WP_068169806.1 HTA01S_RS09255 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 533.3 0.0 2.4e-164 2.4e-164 4 480 .. 16 505 .. 13 506 .] 0.98 Alignments for each domain: == domain 1 score: 533.3 bits; conditional E-value: 2.4e-164 TIGR00133 4 yelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnski 72 ye+viG+E+H ql t+sK+F+++++ + +pNt+ c+v+l+lPG+lPv+N+ av++A+ l+lal+s+ lcl|NCBI__GCF_001592305.1:WP_068169806.1 16 YEVVIGFETHAQLATQSKIFSRAPTAFGA-EPNTQACAVDLALPGTLPVMNRGAVEHAIRLGLALGSH- 82 99*************************99.**************************************. PP TIGR00133 73 vsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdkd 141 ++e svF+RK+YfYpDlPkgyqi+q+++P++++G+++ l +++k++++ r hlEeD+gks ++e + lcl|NCBI__GCF_001592305.1:WP_068169806.1 83 IAEQSVFARKNYFYPDLPKGYQISQFEIPVVQGGEVSFFLGDEKKTVRLVRAHLEEDAGKSLHEEFH-- 149 668*************************************************************775.. PP TIGR00133 142 kqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqe 210 +s +D+NR+g+PLlEiVt+Pd++s+ ea+a+ k+l++i+ ++++ dg+++eGs+R+D+Nvs+r k + lcl|NCBI__GCF_001592305.1:WP_068169806.1 150 GMSGIDLNRAGTPLLEIVTEPDMRSSAEAVAYAKELHKIVTWIGVCDGNMQEGSFRCDANVSVR-KPGD 217 79**************************************************************.5556 PP TIGR00133 211 kegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpe 279 gtr EiKNlns+k +++ai+yE+ q++ +++g+ ++q+t fd + t ++R Ke+++DYRYfp+ lcl|NCBI__GCF_001592305.1:WP_068169806.1 218 PLGTRREIKNLNSFKFMQQAIDYEVRWQIEQIEDGHAIQQATVLFDPDTGETRAMRTKEDAADYRYFPD 286 789999*************************************************************** PP TIGR00133 280 PdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepkla 348 Pdlpp++i+ ++v++ v++ +pelP+++ +r++++y l e+da +l++ ++ +fe+++k+ ++pkl+ lcl|NCBI__GCF_001592305.1:WP_068169806.1 287 PDLPPLVIARDWVEQ-VKAGMPELPRQMAERFVRDYALPEYDATTLTQSPAMAAYFETAAKACGQPKLV 354 ***************.***************************************************** PP TIGR00133 349 vnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellen............. 404 nWi+ e+ ++Ln+ +i + +a ++p++l e+i i g+i++ ak+l+++l ++ lcl|NCBI__GCF_001592305.1:WP_068169806.1 355 SNWIMGEMSRRLNAGEIGIDHAPVSPKQLGEIITNIVSGTINNGGAKQLFDHLWQHpaqvgqassldpv 423 ********************************************************************* PP TIGR00133 405 ......kkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgra 467 +++ ++i+ lgl q++d +l ki++ev++ n+++v ++++gk+ka++ lvGqvmk +kg+a lcl|NCBI__GCF_001592305.1:WP_068169806.1 424 tqfgnpTTSVAEMIDSLGLKQMNDAGALEKIIDEVMAANADNVAQFRAGKDKAFNALVGQVMKASKGKA 492 ***999999************************************************************ PP TIGR00133 468 dpkevekllkell 480 +p++v+ ll+++l lcl|NCBI__GCF_001592305.1:WP_068169806.1 493 NPQQVNDLLRQKL 505 *********9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (506 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: 10.98 // [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