Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate 17910 b3870 glutamine synthetase (NCBI)
Query= CharProtDB::CH_024014 (469 letters) >FitnessBrowser__Keio:17910 Length = 469 Score = 949 bits (2454), Expect = 0.0 Identities = 469/469 (100%), Positives = 469/469 (100%) Query: 1 MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60 MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG Sbjct: 1 MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60 Query: 61 INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTG 120 INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTG Sbjct: 61 INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTG 120 Query: 121 IADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGY 180 IADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGY Sbjct: 121 IADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGY 180 Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK Sbjct: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240 Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIG 300 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIG Sbjct: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIG 300 Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVR 360 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVR Sbjct: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVR 360 Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN Sbjct: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420 Query: 421 ELDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469 ELDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV Sbjct: 421 ELDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469 Lambda K H 0.318 0.136 0.400 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: 925 Number of extensions: 23 Number of successful extensions: 1 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: 469 Length of database: 469 Length adjustment: 33 Effective length of query: 436 Effective length of database: 436 Effective search space: 190096 Effective search space used: 190096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
Align candidate 17910 b3870 (glutamine synthetase (NCBI))
to HMM TIGR00653 (glnA: glutamine synthetase, type I (EC 6.3.1.2))
# 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/TIGR00653.hmm # target sequence database: /tmp/gapView.6635.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00653 [M=462] Accession: TIGR00653 Description: GlnA: glutamine synthetase, type I 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-224 732.1 0.0 1.4e-224 731.9 0.0 1.0 1 lcl|FitnessBrowser__Keio:17910 b3870 glutamine synthetase (NCBI Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17910 b3870 glutamine synthetase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 731.9 0.0 1.4e-224 1.4e-224 1 462 [] 4 468 .. 4 468 .. 0.99 Alignments for each domain: == domain 1 score: 731.9 bits; conditional E-value: 1.4e-224 TIGR00653 1 eevlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvivPfra 79 e+vl++l+e++vkfvdlrf+D+kGk+++v+ip++++++e++eeg++FDgss+ G+k+i+esD++l+pd++t+vi+Pf a lcl|FitnessBrowser__Keio:17910 4 EHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGINESDMVLMPDASTAVIDPFFA 82 578999************************************************************************* PP TIGR00653 80 ekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdseegewn. 156 +++l+++cd+ ep t + y+rdpRsiakrae++l+ t+++d+v fGpE+EFflfd+++f+++ + s++++d++eg+wn lcl|FitnessBrowser__Keio:17910 83 DSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRsTGIADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNs 161 ******************************************************************************9 PP TIGR00653 157 .reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdklvkaaDeivlyK 233 +++e+gnkg++++ kggYf+v+pvD+a+dir+e++l++e++gl ve++HHEvata q+E++++f++++k+aDei++yK lcl|FitnessBrowser__Keio:17910 162 sTQYEGGNKGHRPAVKGGYFPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAgQNEVATRFNTMTKKADEIQIYK 240 99999************************************************************************** PP TIGR00653 234 yvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHakalaAltnptvn 312 yvv+nva++ GktatFmpKp+fgdngsGmH+h+sl+k+g nlfag++ yagLse+alyyigG++kHaka++Al+npt+n lcl|FitnessBrowser__Keio:17910 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDK-YAGLSEQALYYIGGVIKHAKAINALANPTTN 318 ***********************************************.******************************* PP TIGR00653 313 sYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknl 391 sYkRLvpGyEAPv+laysa+nRsa+iRiP++++pka+RiEvR+pDp+anpYL+faallmAgldGiknki+pge++dknl lcl|FitnessBrowser__Keio:17910 319 SYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVRFPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNL 397 ******************************************************************************* PP TIGR00653 392 yelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 y+l++ee+ke i+q++ sLeeal+el+ d+ +++++v+++e+i+a+i+l+r+E +++r+++hpvE+e y++ lcl|FitnessBrowser__Keio:17910 398 YDLPPEEAKE--IPQVAGSLEEALNELDLDRefLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYS 468 **********..*******************888899**********************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (469 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: 11.15 // [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