Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate PP_5046 PP_5046 glutamine synthetase
Query= SwissProt::Q3V5W6 (468 letters) >FitnessBrowser__Putida:PP_5046 Length = 468 Score = 901 bits (2328), Expect = 0.0 Identities = 434/468 (92%), Positives = 454/468 (97%) Query: 1 MSKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGI 60 MSKSVQLIKDHDVKWIDLRFTDTKG QHHVTMP+RDAL++DFFEVGKMFDGSSIAGWKGI Sbjct: 1 MSKSVQLIKDHDVKWIDLRFTDTKGIQHHVTMPSRDALDEDFFEVGKMFDGSSIAGWKGI 60 Query: 61 EASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGI 120 EASDMIL+P D+TAVLDPFTE+ TLI+ CDI++PS+MQGYDRDPRAIA RAEEYLK+TGI Sbjct: 61 EASDMILMPVDETAVLDPFTEEPTLIITCDIVDPSSMQGYDRDPRAIAKRAEEYLKSTGI 120 Query: 121 GDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYF 180 GDTVFAGPEPEFFIFDEVKF SDISGSMFKI+SEQGSWM+ D+EGGNKGHRPGVKGGYF Sbjct: 121 GDTVFAGPEPEFFIFDEVKFHSDISGSMFKIFSEQGSWMTGADVEGGNKGHRPGVKGGYF 180 Query: 181 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKY 240 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQ LKY Sbjct: 181 PVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQALKY 240 Query: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGG 300 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSI KDGKNTF+GEGYAGLS+TALYFIGG Sbjct: 241 VVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIWKDGKNTFSGEGYAGLSDTALYFIGG 300 Query: 301 IIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARF 360 IIKHGKALNGFTNP+TNSYKRLVPGFEAPVMLAYSARNRSASIRIPYV SP+ RRIEARF Sbjct: 301 IIKHGKALNGFTNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVGSPKARRIEARF 360 Query: 361 PDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEE 420 PDP+ANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAK IPQVCGSLKEALEE Sbjct: 361 PDPSANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKNIPQVCGSLKEALEE 420 Query: 421 LDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYSC 468 LDKGRAFLTKGGVFSDDFIDA+I LKSEEEIKVRTFVHPLEYELYYSC Sbjct: 421 LDKGRAFLTKGGVFSDDFIDAFIELKSEEEIKVRTFVHPLEYELYYSC 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: 947 Number of extensions: 33 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 PP_5046 PP_5046 (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.1608.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-205 667.6 0.0 4.9e-205 667.5 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_5046 PP_5046 glutamine synthetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_5046 PP_5046 glutamine synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 667.5 0.0 4.9e-205 4.9e-205 4 462 .] 5 467 .. 2 467 .. 0.99 Alignments for each domain: == domain 1 score: 667.5 bits; conditional E-value: 4.9e-205 TIGR00653 4 lkllkeenvkfvdlrfvDikGklkkveipvs.eleeealeegiaFDgssveGfksieesDlllkpdpetlvivPf 77 ++l+k+++vk +dlrf+D+kG+ ++v++p + +l+e+++e g++FDgss+ G+k+ie sD++l+p+ et+v +Pf lcl|FitnessBrowser__Putida:PP_5046 5 VQLIKDHDVKWIDLRFTDTKGIQHHVTMPSRdALDEDFFEVGKMFDGSSIAGWKGIEASDMILMPVDETAVLDPF 79 6899*************************872578**************************************** PP TIGR00653 78 raekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssflevdse 151 ++e++l+++cd+ +p ++ y+rdpR iakraee+lk t++gd+v+ GpE+EFf+fd+v+f++ + s++++ se lcl|FitnessBrowser__Putida:PP_5046 80 TEEPTLIITCDIVDPSSMQGYDRDPRAIAKRAEEYLKsTGIGDTVFAGPEPEFFIFDEVKFHSDISGSMFKIFSE 154 *************************************************************************** PP TIGR00653 152 egewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvata.qaEidikfdklv 223 +g+w ++ve+gnkg+++ kggYf+v+p D+ ++ir+ +++alee+g +vev+HHEvata q+Ei++kf++lv lcl|FitnessBrowser__Putida:PP_5046 155 QGSWMtgADVEGGNKGHRPGVKGGYFPVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAgQNEIGVKFNTLV 229 ****988999***************************************************************** PP TIGR00653 224 kaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetalyyigGilk 298 k+aDe++ +Kyvv+nva+ +G+tatFmpKpl+gdngsGmHvh+s+wkdg+n f+ge yagLs+taly+igGi+k lcl|FitnessBrowser__Putida:PP_5046 230 KKADEVQALKYVVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIWKDGKNTFSGEG-YAGLSDTALYFIGGIIK 303 ********************************************************9.***************** PP TIGR00653 299 HakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpYLafaallmAg 373 H+kal+ +tnp++nsYkRLvpG+EAPv+laysa+nRsa+iRiP++ +pka+RiE R+pDpsanpYLafaallmAg lcl|FitnessBrowser__Putida:PP_5046 304 HGKALNGFTNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVGSPKARRIEARFPDPSANPYLAFAALLMAG 378 *************************************************************************** PP TIGR00653 374 ldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeelieafielkrkEve 446 ldGi+nki+pg++ dknly+l++ee+k+ i+q+ sL+eal+el++ + +++++v+++++i+afielk +E lcl|FitnessBrowser__Putida:PP_5046 379 LDGIQNKIHPGDAADKNLYDLPPEEAKN--IPQVCGSLKEALEELDKGRafLTKGGVFSDDFIDAFIELKSEEEI 451 ****************************..******************99999********************** PP TIGR00653 447 elrlkvhpvElekyld 462 ++r+ vhp+E e y++ lcl|FitnessBrowser__Putida:PP_5046 452 KVRTFVHPLEYELYYS 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.60 // [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