Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate PfGW456L13_5036 Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7)
Query= SwissProt::Q9RF06 (475 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 Length = 481 Score = 455 bits (1171), Expect = e-132 Identities = 228/481 (47%), Positives = 332/481 (69%), Gaps = 9/481 (1%) Query: 1 MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60 M +E VIGLE+H +L T SK+FS S FG+EPN+ +++DL PGVLPV+N+ AV A+ Sbjct: 1 MQWEVVIGLEIHTQLTTRSKIFSGSSTTFGSEPNTQASLVDLGMPGVLPVLNQEAVRMAV 60 Query: 61 RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119 +A++ EI + F RKNYFYPD PK YQISQ + PI G++DI + DG KR+GIT Sbjct: 61 MFGLAIDAEIGQHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIALEDGTVKRVGIT 120 Query: 120 RLHMEEDAGKSTHKGEYSL---VDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQY 176 R H+EEDAGKS H+ E+S +DLNR GTPL+EIVSEPD+RS KEA AY++ + ++++Y Sbjct: 121 RAHLEEDAGKSLHE-EFSGATGIDLNRAGTPLLEIVSEPDMRSAKEAVAYVKAIHALVRY 179 Query: 177 TGVSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELL 236 G+ D M EGSLRCD N+S+RP GQ +FGT+ E+KN+NSF ++ K + E +RQ E + Sbjct: 180 LGICDGNMAEGSLRCDCNVSIRPKGQVEFGTRCEIKNVNSFRFIEKAINSEIQRQIELIE 239 Query: 237 SGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELP 296 GG++ Q+TR +D + +T MR KE ++DYRYFP+PD++P+ I++++ + VR T+PELP Sbjct: 240 DGGKVIQQTRLYDPNKDETRPMRSKEEANDYRYFPDPDLLPVVIENSFLDDVRATLPELP 299 Query: 297 DERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQ 356 +++ ++ + GL YDA VL ++E +D+FE G D KL +NW+M + LNK Sbjct: 300 PQKRERFQEQFGLSVYDASVLATSREQADYFEKVASIGGDAKLAANWVMVELGSLLNKQG 359 Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEA 416 +++ ++ ++ E L GM+ I+D T+S KIAK VF +A G+A +I++ GL Q++D Sbjct: 360 LDIEESPVSAELLGGMLLRIKDNTISGKIAKVVFEAMANGEGSADEIIDKRGLKQVTDTG 419 Query: 417 TLLKFVNEALDNNEQSVEDYKNG----KGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472 + ++E L N + VE Y+ +GK GF VGQ MKASKG+ANPQ VN+LLK +L Sbjct: 420 AISAVLDEMLAANAEQVEQYRAADEAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSKL 479 Query: 473 D 473 + Sbjct: 480 E 480 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: 630 Number of extensions: 20 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: 481 Length adjustment: 34 Effective length of query: 441 Effective length of database: 447 Effective search space: 197127 Effective search space used: 197127 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 PfGW456L13_5036 (Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit B (EC 6.3.5.7))
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.21157.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-174 565.2 0.0 5.8e-174 565.0 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 Aspartyl-tRNA(Asn) amidotransfer Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 Aspartyl-tRNA(Asn) amidotransferase subunit B (EC 6.3.5.6) @ # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 565.0 0.0 5.8e-174 5.8e-174 2 480 .. 1 479 [. 1 480 [. 0.98 Alignments for each domain: == domain 1 score: 565.0 bits; conditional E-value: 5.8e-174 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNke 56 +++e+viGlE+H+ql t+sK+F+ +s+ + + +pNt+ + v+lg+PG+lPvlN+e lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 1 MQWEVVIGLEIHTQLTTRSKIFSGSSTTFGS-EPNTQASLVDLGMPGVLPVLNQE 54 5789***************************.*********************** PP TIGR00133 57 avkkAlklalalnskivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleie 111 av++A++ +la++++i + vF+RK+YfYpDlPkgyqi+q +lPi+ +G+l+i lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 55 AVRMAVMFGLAIDAEIG-QHNVFARKNYFYPDLPKGYQISQMELPIVGKGHLDIA 108 ***************55.79*********************************** PP TIGR00133 112 leeke.keigierlhlEeDtgksqykesdkdkqslvDfNRsgvPLlEiVtkPdlk 165 le++ k++gi+r hlEeD+gks ++e + + +D+NR+g+PLlEiV++Pd++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 109 LEDGTvKRVGITRAHLEEDAGKSLHEEFS--GATGIDLNRAGTPLLEIVSEPDMR 161 999888********************775..7999******************** PP TIGR00133 166 sakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKN 220 sakea+a++k +++++ryl+i dg++ eGs+R+D+Nvsir+kGq ++gtr EiKN lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 162 SAKEAVAYVKAIHALVRYLGICDGNMAEGSLRCDCNVSIRPKGQVEFGTRCEIKN 216 ******************************************************* PP TIGR00133 221 lnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYR 275 +ns++ iekai+ Ei+Rq++l+++g +v q+tr +d +k t +R+Kee++DYR lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 217 VNSFRFIEKAINSEIQRQIELIEDGGKVIQQTRLYDPNKDETRPMRSKEEANDYR 271 ******************************************************* PP TIGR00133 276 YfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdle 330 Yfp+Pdl p++i+++++++ v+++lpelP +kr+r+++++gls +da vl + +e lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 272 YFPDPDLLPVVIENSFLDD-VRATLPELPPQKRERFQEQFGLSVYDASVLATSRE 325 ****************999.*********************************** PP TIGR00133 331 lldafeevvklikepklavnWileellgeLnkkkislaeallkpeelaeliklik 385 +d+fe+v++ +++kla+nW++ el + Lnk+ ++++e+ +++e l ++ ik lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 326 QADYFEKVASIGGDAKLAANWVMVELGSLLNKQGLDIEESPVSAELLGGMLLRIK 380 ******************************************************* PP TIGR00133 386 egkisqksakelleellenkkdpkklieklgliqisdekelvkiveevikenpke 440 +++is+k+ak ++e + + +++++++i+k+gl q++d+ ++ ++++e+++ n+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 381 DNTISGKIAKVVFEAMANGEGSADEIIDKRGLKQVTDTGAISAVLDEMLAANAEQ 435 ******************************************************* PP TIGR00133 441 vekyk....sgkekalkflvGqvmkktkgradpkevekllkell 480 ve+y+ +++ k+++f+vGq+mk +kg+a+p++v++llk +l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5036 436 VEQYRaadeAKRGKMFGFFVGQAMKASKGKANPQQVNELLKSKL 479 ****9888778899***************************988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (481 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: 12.10 // [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