Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate 3607799 Dshi_1207 glutamyl-tRNA(Gln) amidotransferase, B subunit (RefSeq)
Query= SwissProt::Q9RF06 (475 letters) >FitnessBrowser__Dino:3607799 Length = 505 Score = 395 bits (1016), Expect = e-114 Identities = 208/483 (43%), Positives = 303/483 (62%), Gaps = 14/483 (2%) Query: 3 FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62 +E VIGLEVH ++ T++K+FS + FGAEPNSN +D PG+LPV+N+ V A+R Sbjct: 21 WELVIGLEVHAQVATNAKLFSGASTLFGAEPNSNVAFVDAGMPGMLPVINEECVAQAVRT 80 Query: 63 AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121 + L I S FDRKNYFYPD P+ YQISQ PI G + +E+ DG + + I R+ Sbjct: 81 GLGLKAAINLTSAFDRKNYFYPDLPQGYQISQLYHPIVGEGEVLVELGDGTARVVRIERI 140 Query: 122 HMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179 H+E+DAGKS H + S VDLNR G L+EIVS PDIR P+EA AY+ KLR I++Y G Sbjct: 141 HLEQDAGKSIHDMDPHMSFVDLNRTGVALMEIVSRPDIRGPEEAAAYVSKLRQIMRYLGT 200 Query: 180 SDVKMEEGSLRCDANISL-RPYGQEKF---------GTKAELKNLNSFNYVRKGLEYEEK 229 D M+ G+LR D N+S+ RP EK+ GT+ E+KN+NS ++++ +EYE + Sbjct: 201 CDGNMQNGNLRADVNVSVCRPGDYEKYQASQDFSHLGTRCEIKNMNSLRFIQQAIEYEAR 260 Query: 230 RQEEELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVR 289 RQ + GG + QETR +D G+T MR KE + DYRYFP+PD++PL I+ AW + + Sbjct: 261 RQIAIIEDGGSVTQETRLYDPDKGETRSMRSKEEAHDYRYFPDPDLLPLEIEQAWVDDIA 320 Query: 290 QTIPELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVN 349 +PELPD +KA+++ E GL YDA VLT + +FE+ D KL +NW++ + Sbjct: 321 AALPELPDAKKARFITEFGLSDYDASVLTADTTNAAYFEAVAGEAGDGKLAANWVINELF 380 Query: 350 EYLNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGL 409 L K ++ ++ ++P LAG+IKLI+ +S KIAK +F + +GG+ +I+E G+ Sbjct: 381 GRLKKEDHDITESPVSPAQLAGIIKLIKADAISGKIAKDLFEIVYTEGGDPAEIVEARGM 440 Query: 410 VQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLK 469 Q++D + V+E + N V + K G+ VGQ+MKA+ G+ANP+ VNQ++ Sbjct: 441 KQVTDTGAIEAAVDEIIAANPAQVAKAQENP-KLAGWFVGQVMKATGGKANPKAVNQIVA 499 Query: 470 QEL 472 +L Sbjct: 500 AKL 502 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: 638 Number of extensions: 28 Number of successful extensions: 5 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: 505 Length adjustment: 34 Effective length of query: 441 Effective length of database: 471 Effective search space: 207711 Effective search space used: 207711 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 3607799 Dshi_1207 (glutamyl-tRNA(Gln) amidotransferase, B subunit (RefSeq))
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.930701.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-164 532.6 0.0 4.7e-164 532.4 0.0 1.0 1 FitnessBrowser__Dino:3607799 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Dino:3607799 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 532.4 0.0 4.7e-164 4.7e-164 2 480 .. 19 502 .. 18 503 .. 0.95 Alignments for each domain: == domain 1 score: 532.4 bits; conditional E-value: 4.7e-164 TIGR00133 2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsevsvFdRK 82 +++elviGlEvH q+ t++KlF+ +s+ + +pN+nv v+ g+PG lPv+N+e v++A+ +l l++ i+ +s FdRK FitnessBrowser__Dino:3607799 19 EDWELVIGLEVHAQVATNAKLFSGASTLFGA-EPNSNVAFVDAGMPGMLPVINEECVAQAVRTGLGLKAAIN-LTSAFDRK 97 5789*************************99.**************************************76.59****** PP TIGR00133 83 hYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesdkdkqslvDfNRsgvPLlEiVtkP 162 +YfYpDlP+gyqi+q + Pi+ +G++ +el ++ + ++ier+hlE+D+gks + + +++s+vD+NR+gv L+EiV++P FitnessBrowser__Dino:3607799 98 NYFYPDLPQGYQISQLYHPIVGEGEVLVELGDGTaRVVRIERIHLEQDAGKSIHDMD--PHMSFVDLNRTGVALMEIVSRP 176 *****************************977654999****************976..78******************** PP TIGR00133 163 dlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGq..........ekegtrvEiKNlnslksiekaiey 233 d++ ++ea+a+++klrqi+ryl+ dg++++G++R+DvNvs+ G+ ++ gtr EiKN+nsl+ i++aiey FitnessBrowser__Dino:3607799 177 DIRGPEEAAAYVSKLRQIMRYLGTCDGNMQNGNLRADVNVSVCRPGDyekyqasqdfSHLGTRCEIKNMNSLRFIQQAIEY 257 ******************************************87765222222222245689******************* PP TIGR00133 234 EieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekveeklpelPeakrirlkke 314 E Rq++++++g +v+qetr +d k t s+R+Kee++DYRYfp+Pdl p+ei++ +v++ +++ lpelP+ak++r+ +e FitnessBrowser__Dino:3607799 258 EARRQIAIIEDGGSVTQETRLYDPDKGETRSMRSKEEAHDYRYFPDPDLLPLEIEQAWVDD-IAAALPELPDAKKARFITE 337 ************************************************************9.******************* PP TIGR00133 315 yglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksak 395 +gls++da vl++d++ + +fe v+ +++ kla+nW+++el g+L+k++ +++e+ ++p +la +iklik++ is+k+ak FitnessBrowser__Dino:3607799 338 FGLSDYDASVLTADTTNAAYFEAVAGEAGDGKLAANWVINELFGRLKKEDHDITESPVSPAQLAGIIKLIKADAISGKIAK 418 ********************************************************************************* PP TIGR00133 396 elleellenkkdpkklieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekll 476 +l+e + ++++dp +++e++g+ q++d+ ++ ++v+e+i+ np +v k +++ k+ +++vGqvmk t g+a+pk v++++ FitnessBrowser__Dino:3607799 419 DLFEIVYTEGGDPAEIVEARGMKQVTDTGAIEAAVDEIIAANPAQVAKAQEN-PKLAGWFVGQVMKATGGKANPKAVNQIV 498 **********************************************998765.67889**********************9 PP TIGR00133 477 kell 480 +l FitnessBrowser__Dino:3607799 499 AAKL 502 8877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (505 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 22.09 // [ok]
This GapMind analysis is from Jul 25 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