Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate Ga0059261_0083 Ga0059261_0083 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (EC 6.3.5.-)
Query= SwissProt::Q9RF06 (475 letters) >FitnessBrowser__Korea:Ga0059261_0083 Length = 486 Score = 421 bits (1082), Expect = e-122 Identities = 220/473 (46%), Positives = 313/473 (66%), Gaps = 4/473 (0%) Query: 3 FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62 +E VIGLEVH ++ +++K+FS + FGAEPN+ ++ID A PG+LPV N+ + A+R Sbjct: 15 WEVVIGLEVHAQVTSNAKLFSGAATEFGAEPNTQVSLIDAAMPGMLPVPNRECIRQAVRT 74 Query: 63 AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVDGETKRIGITRLH 122 MA++ +I S+FDRKNYFY D P+ YQISQ P+ G I+IEVDGETK IG+ R+H Sbjct: 75 GMAIDAQINKWSRFDRKNYFYADLPQGYQISQLYHPLVGEGEIEIEVDGETKTIGVERIH 134 Query: 123 MEEDAGKSTH--KGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGVS 180 +E+DAGK H S VDLNR G L+EIVS+PD+RSP EA AYL KLRSI++Y G Sbjct: 135 VEQDAGKLMHDQHPRLSYVDLNRSGVALMEIVSKPDMRSPAEAGAYLSKLRSILRYVGSC 194 Query: 181 DVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGGE 240 D M++GS+R D N+S+R G E FGT+ E KN+NS +V + +E E RQ + + SGG+ Sbjct: 195 DGNMDQGSMRADVNVSVRRPG-EAFGTRTETKNVNSVRFVMQTVEIEALRQIDVIESGGK 253 Query: 241 IGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDERK 300 I QETR FD G+T MR KE + DYRYFP+PD++PL +DDA+ E R ++PELPD ++ Sbjct: 254 IVQETRLFDPDKGETRSMRSKEDAHDYRYFPDPDLLPLELDDAFLEECRGSLPELPDAKR 313 Query: 301 AKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVELL 360 A+Y+ LG+ Y+A VLT E + +F++ ++ GA +NW+ + LNK ++ Sbjct: 314 ARYL-ALGITPYNAGVLTAEVESARYFDALLDAGAKGPAAANWVTSELFGALNKLGKDIE 372 Query: 361 DTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLLK 420 ++ ++P A ++ L+ DGT+S +AK+VF + GG+ I+E+ GL Q SD + Sbjct: 373 NSPVSPAQAAELLGLVADGTISGSLAKQVFEIMLETGGSPSAIVEERGLKQTSDTGAIEA 432 Query: 421 FVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473 + E L N +E Y+ GK GF VGQ MKA G+ANP +VN+LLK+ L+ Sbjct: 433 VIAEVLAKNPGQLEQYRGGKEALFGFFVGQTMKAMGGKANPGVVNELLKKALN 485 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: 635 Number of extensions: 22 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: 486 Length adjustment: 34 Effective length of query: 441 Effective length of database: 452 Effective search space: 199332 Effective search space used: 199332 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: 51 (24.3 bits)
Align candidate Ga0059261_0083 Ga0059261_0083 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B (EC 6.3.5.-))
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.7497.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-163 528.2 0.0 9.6e-163 528.0 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0083 Ga0059261_0083 aspartyl/glutamyl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0083 Ga0059261_0083 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B ( # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 528.0 0.0 9.6e-163 9.6e-163 3 481 .] 14 485 .. 12 485 .. 0.98 Alignments for each domain: == domain 1 score: 528.0 bits; conditional E-value: 9.6e-163 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 e+e+viGlEvH q+ ++KlF+ + +e+ +pNt+v+ ++ ++PG lPv+N+e +++A+ ++a++++ lcl|FitnessBrowser__Korea:Ga0059261_0083 14 EWEVVIGLEVHAQVTSNAKLFSGAATEFGA-EPNTQVSLIDAAMPGMLPVPNRECIRQAVRTGMAIDAQ 81 689*************************99.************************************** PP TIGR00133 72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesdk 140 i+ + s FdRK+YfY DlP+gyqi+q + P++ +G++eie++++ k+ig+er+h+E+D+gk+++ ++ lcl|FitnessBrowser__Korea:Ga0059261_0083 82 IN-KWSRFDRKNYFYADLPQGYQISQLYHPLVGEGEIEIEVDGETKTIGVERIHVEQDAGKLMHDQH-- 147 66.6************************************************************976.. PP TIGR00133 141 dkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq 209 ++ s+vD+NRsgv L+EiV+kPd++s+ ea a+l+klr+ilry++ dg++++GsmR+DvNvs+r + lcl|FitnessBrowser__Korea:Ga0059261_0083 148 PRLSYVDLNRSGVALMEIVSKPDMRSPAEAGAYLSKLRSILRYVGSCDGNMDQGSMRADVNVSVR-RPG 215 68***************************************************************.556 PP TIGR00133 210 ekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfp 278 e++gtr E KN+ns++ + + +e E Rq++++++g +++qetr fd k t s+R+Ke+++DYRYfp lcl|FitnessBrowser__Korea:Ga0059261_0083 216 EAFGTRTETKNVNSVRFVMQTVEIEALRQIDVIESGGKIVQETRLFDPDKGETRSMRSKEDAHDYRYFP 284 78******************************************************************* PP TIGR00133 279 ePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepkl 347 +Pdl p+e+d+ +++e ++ lpelP+akr+r+ +g+ + a vl++++e +++f+ + + ++ + lcl|FitnessBrowser__Korea:Ga0059261_0083 285 DPDLLPLELDDAFLEE-CRGSLPELPDAKRARYL-ALGITPYNAGVLTAEVESARYFDALLDAGAKGPA 351 *************999.***************98.59******************************** PP TIGR00133 348 avnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkklieklg 416 a+nW+++el g Lnk +++++ ++p + ael+ l+ +g+is+ ak+++e +le++++p++++e++g lcl|FitnessBrowser__Korea:Ga0059261_0083 352 AANWVTSELFGALNKLGKDIENSPVSPAQAAELLGLVADGTISGSLAKQVFEIMLETGGSPSAIVEERG 420 ********************************************************************* PP TIGR00133 417 liqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkells 481 l q sd+ ++ +++ ev+++np+++e+y+ gke++++f+vGq mk g+a+p v++llk+ l+ lcl|FitnessBrowser__Korea:Ga0059261_0083 421 LKQTSDTGAIEAVIAEVLAKNPGQLEQYRGGKEALFGFFVGQTMKAMGGKANPGVVNELLKKALN 485 **************************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (486 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: 9.80 // [ok]
This GapMind analysis is from Apr 09 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