Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate GFF325 PS417_01655 glutamine synthetase
Query= SwissProt::Q3V5W6 (468 letters) >FitnessBrowser__WCS417:GFF325 Length = 468 Score = 904 bits (2337), Expect = 0.0 Identities = 435/468 (92%), Positives = 454/468 (97%) Query: 1 MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGI 60 MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDAL++ FFE GKMFDGSSIAGWKGI Sbjct: 1 MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALDEAFFEEGKMFDGSSIAGWKGI 60 Query: 61 EASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGI 120 EASDMIL+PDD TAVLDPFTE+ TLILVCD+IEPSTMQGYDRDPRAIA RAEEYLK+TGI Sbjct: 61 EASDMILMPDDSTAVLDPFTEEPTLILVCDVIEPSTMQGYDRDPRAIAKRAEEYLKSTGI 120 Query: 121 GDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYF 180 GDTVF GPEPEFFIFD+VKFKSDISGSMFKIYSEQGSWMSDQD+EGGN GHRPG+KGGYF Sbjct: 121 GDTVFVGPEPEFFIFDQVKFKSDISGSMFKIYSEQGSWMSDQDVEGGNHGHRPGIKGGYF 180 Query: 181 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKY 240 PVPPFDHDHEIRT+MCNA+E+MG T+EVHHHEVATAGQNEIGVKFNTLV KADEVQTLKY Sbjct: 181 PVPPFDHDHEIRTSMCNAMEDMGLTIEVHHHEVATAGQNEIGVKFNTLVAKADEVQTLKY 240 Query: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGG 300 VHN A AYGRTATFMPKPLYGDNGSGMHVH+SIAK+GKNTFAGEGYAGLS+TALYFIGG Sbjct: 241 CVHNTAVAYGRTATFMPKPLYGDNGSGMHVHLSIAKEGKNTFAGEGYAGLSDTALYFIGG 300 Query: 301 IIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARF 360 IIKHGKALNGFTNP+TNSYKRLVPGFEAPVMLAYSARNRSASIRIPYV+SPR RRIEARF Sbjct: 301 IIKHGKALNGFTNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVSSPRARRIEARF 360 Query: 361 PDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 420 PDPAANPYLAFAAL+MAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE Sbjct: 361 PDPAANPYLAFAALVMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 420 Query: 421 LDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYSC 468 LDKGRAFLTKGGVFSDDFIDAYI LKSEEEIKVRTFVHPLEYELYYSC Sbjct: 421 LDKGRAFLTKGGVFSDDFIDAYIGLKSEEEIKVRTFVHPLEYELYYSC 468 Lambda K H 0.318 0.137 0.409 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: 933 Number of extensions: 36 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: 468 Length of database: 468 Length adjustment: 33 Effective length of query: 435 Effective length of database: 435 Effective search space: 189225 Effective search space used: 189225 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 GFF325 PS417_01655 (glutamine synthetase)
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.3703.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-203 661.1 0.0 4.8e-203 660.9 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF325 PS417_01655 glutamine synthetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF325 PS417_01655 glutamine synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 660.9 0.0 4.8e-203 4.8e-203 4 462 .] 5 467 .. 2 467 .. 0.98 Alignments for each domain: == domain 1 score: 660.9 bits; conditional E-value: 4.8e-203 TIGR00653 4 lkllkeenvkfvdlrfvDikGklkkveipvse.leeealeegiaFDgssveGfksieesDlllkpdpetlvivPfr 78 ++l+k+++vk +dlrf+D+kG+ ++v++p+++ l+e ++eeg++FDgss+ G+k+ie sD++l+pd +t+v +Pf+ lcl|FitnessBrowser__WCS417:GFF325 5 VQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDaLDEAFFEEGKMFDGSSIAGWKGIEASDMILMPDDSTAVLDPFT 80 6899*************************985267999************************************** PP TIGR00653 79 aekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdseeg 153 +e++l+++cdv ep t++ y+rdpR iakraee+lk t++gd+v++GpE+EFf+fd+v+fk+ + s++++ se+g lcl|FitnessBrowser__WCS417:GFF325 81 EEPTLILVCDVIEPSTMQGYDRDPRAIAKRAEEYLKsTGIGDTVFVGPEPEFFIFDQVKFKSDISGSMFKIYSEQG 156 **************************************************************************** PP TIGR00653 154 ewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdklvkaa 226 +w ++ve+gn+g+++ kggYf+v+p D+ ++ir+++++a+e++gl++ev+HHEvata q+Ei++kf++lv +a lcl|FitnessBrowser__WCS417:GFF325 157 SWMsdQDVEGGNHGHRPGIKGGYFPVPPFDHDHEIRTSMCNAMEDMGLTIEVHHHEVATAgQNEIGVKFNTLVAKA 232 **988899999***************************************************************** PP TIGR00653 227 DeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilkHaka 302 De++++Ky v+n+a +G+tatFmpKpl+gdngsGmHvhls+ k+g+n fage yagLs+taly+igGi+kH+ka lcl|FitnessBrowser__WCS417:GFF325 233 DEVQTLKYCVHNTAVAYGRTATFMPKPLYGDNGSGMHVHLSIAKEGKNTFAGEG-YAGLSDTALYFIGGIIKHGKA 307 *****************************************************9.********************* PP TIGR00653 303 laAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAgldGik 378 l+ +tnp++nsYkRLvpG+EAPv+laysa+nRsa+iRiP++++p+a+RiE R+pDp+anpYLafaal+mAgldGi+ lcl|FitnessBrowser__WCS417:GFF325 308 LNGFTNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVSSPRARRIEARFPDPAANPYLAFAALVMAGLDGIQ 383 **************************************************************************** PP TIGR00653 379 nkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEveelrlkv 452 nki+pg++ dknly+l++ee+ke i+q+ sL+eal+el++ + +++++v+++++i+a+i lk +E ++r+ v lcl|FitnessBrowser__WCS417:GFF325 384 NKIHPGDAADKNLYDLPPEEAKE--IPQVCGSLKEALEELDKGRafLTKGGVFSDDFIDAYIGLKSEEEIKVRTFV 457 ***********************..******************99999**************************** PP TIGR00653 453 hpvElekyld 462 hp+E e y++ lcl|FitnessBrowser__WCS417:GFF325 458 HPLEYELYYS 467 ********95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (468 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: 12.21 // [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