Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate AZOBR_RS20650 AZOBR_RS20650 glutamyl-tRNA amidotransferase subunit B
Query= SwissProt::Q9RF06 (475 letters) >FitnessBrowser__azobra:AZOBR_RS20650 Length = 483 Score = 440 bits (1131), Expect = e-128 Identities = 221/473 (46%), Positives = 324/473 (68%), Gaps = 5/473 (1%) Query: 3 FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62 +E VIGLEVH ++ +++K+FS + FGAEPNS + +D A+PG+LPV+N+R ++ A+R Sbjct: 11 WEIVIGLEVHAQVISNAKLFSGAATAFGAEPNSQVSFVDAAFPGMLPVINERCIEQAVRT 70 Query: 63 AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGITRL 121 + L +I S FDRKNYFY D P+ YQISQ+ QPI G I +++ DG ++ +G+TRL Sbjct: 71 GLGLKAQINLHSVFDRKNYFYADLPQGYQISQYLQPIVGKGEIVLDLPDGSSRTVGVTRL 130 Query: 122 HMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179 H+E+DAGKS H + +DLNR G L+EIVSEPD+R+ +EA AY+ KLRSI++Y G Sbjct: 131 HLEQDAGKSLHDQHPAKTYIDLNRSGVALMEIVSEPDMRTAEEAGAYVRKLRSILRYLGT 190 Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSGG 239 D MEEGS+RCD N+S+R G FGT+ E+KN+NS +V + +EYE +RQ E + GG Sbjct: 191 CDGNMEEGSMRCDVNVSVRKPGAP-FGTRCEIKNVNSIRFVMQAIEYEARRQIEIIEEGG 249 Query: 240 EIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDER 299 +I QETR +D + T MR KE + DYRYFP+PD++PL +D W E +++T+PELPD++ Sbjct: 250 KIDQETRLWDTTKFVTRSMRSKEEAHDYRYFPDPDLLPLELDADWVEDIKKTLPELPDDK 309 Query: 300 KAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVEL 359 KA++++E L YDA+VL K +DF+E+ + G D KL +NW+ G + YLNK E+ Sbjct: 310 KARFISEYKLSPYDANVLVSEKARADFYEA-VAKGRDPKLAANWVTGELFGYLNKAGKEI 368 Query: 360 LDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEATLL 419 ++ ++ ENL G+I LI D T+S +IAK+VF + G I+E GL Q++D + Sbjct: 369 EESPVSAENLGGLIDLIADNTISGRIAKEVFEAMFETGEKPADIVEKKGLRQVTDTGAIE 428 Query: 420 KFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472 ++ L N V ++++GK K GF VGQ+MKA++G+ANP LVN++L +L Sbjct: 429 SSIDAVLAANADKVAEFRSGKDKLFGFFVGQVMKATQGKANPALVNEILMAKL 481 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: 616 Number of extensions: 27 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: 483 Length adjustment: 34 Effective length of query: 441 Effective length of database: 449 Effective search space: 198009 Effective search space used: 198009 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 AZOBR_RS20650 AZOBR_RS20650 (glutamyl-tRNA amidotransferase 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.18573.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-168 546.0 0.0 3.9e-168 545.8 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS20650 AZOBR_RS20650 glutamyl-tRNA amid Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS20650 AZOBR_RS20650 glutamyl-tRNA amidotransferase subunit B # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 545.8 0.0 3.9e-168 3.9e-168 3 480 .. 10 481 .. 8 482 .. 0.97 Alignments for each domain: == domain 1 score: 545.8 bits; conditional E-value: 3.9e-168 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnsk 71 ++e+viGlEvH q+ ++KlF+ + + + +pN++v+ v+ ++PG lPv+N++ +++A+ +l l+++ lcl|FitnessBrowser__azobra:AZOBR_RS20650 10 DWEIVIGLEVHAQVISNAKLFSGAATAFGA-EPNSQVSFVDAAFPGMLPVINERCIEQAVRTGLGLKAQ 77 5799************************99.************************************** PP TIGR00133 72 ivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykesd 139 i+ svFdRK+YfY DlP+gyqi+q+ +Pi+ +G++ ++l +++ +++g++rlhlE+D+gks + ++ lcl|FitnessBrowser__azobra:AZOBR_RS20650 78 IN-LHSVFDRKNYFYADLPQGYQISQYLQPIVGKGEIVLDLPDGSsRTVGVTRLHLEQDAGKSLHDQH- 144 77.59***********************************9887659******************966. PP TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208 + +++D+NRsgv L+EiV++Pd+++a+ea a+++klr+ilryl+ dg++eeGsmR+DvNvs+r k lcl|FitnessBrowser__azobra:AZOBR_RS20650 145 -PAKTYIDLNRSGVALMEIVSEPDMRTAEEAGAYVRKLRSILRYLGTCDGNMEEGSMRCDVNVSVR-KP 211 .78***************************************************************.66 PP TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277 +gtr EiKN+ns++ + +aieyE Rq++++++g ++ qetr +d++k +t s+R+Kee++DYRYf lcl|FitnessBrowser__azobra:AZOBR_RS20650 212 GAPFGTRCEIKNVNSIRFVMQAIEYEARRQIEIIEEGGKIDQETRLWDTTKFVTRSMRSKEEAHDYRYF 280 6789***************************************************************** PP TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346 p+Pdl p+e+d ++v++ ++++lpelP+ k++r+ +ey+ls +da+vlvs++ +d +e v+k +pk lcl|FitnessBrowser__azobra:AZOBR_RS20650 281 PDPDLLPLELDADWVED-IKKTLPELPDDKKARFISEYKLSPYDANVLVSEKARADFYEAVAKGR-DPK 347 ****************9.9*************************************999888765.56* PP TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415 la+nW++ el g+Lnk +++e+ +++e+l li+li +++is+++ake++e ++e++++p ++ek+ lcl|FitnessBrowser__azobra:AZOBR_RS20650 348 LAANWVTGELFGYLNKAGKEIEESPVSAENLGGLIDLIADNTISGRIAKEVFEAMFETGEKPADIVEKK 416 ********************************************************************* PP TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480 gl q++d+ ++ + +++v++ n+++v +++sgk+k+++f+vGqvmk t+g+a+p+ v+++l +l lcl|FitnessBrowser__azobra:AZOBR_RS20650 417 GLRQVTDTGAIESSIDAVLAANADKVAEFRSGKDKLFGFFVGQVMKATQGKANPALVNEILMAKL 481 ************************************************************98877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (483 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.19 // [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