Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate WP_086510693.1 BZY95_RS14880 glutamate--ammonia ligase
Query= SwissProt::Q3V5W6 (468 letters) >NCBI__GCF_002151265.1:WP_086510693.1 Length = 468 Score = 731 bits (1888), Expect = 0.0 Identities = 345/467 (73%), Positives = 405/467 (86%), Gaps = 1/467 (0%) Query: 2 SKSVQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGIE 61 +K++ LI++HDVKW+DLRFTDT+G + HVT+PARD + ++FFE G+MFDGSSI GWKGI Sbjct: 3 AKTLALIEEHDVKWVDLRFTDTRGKEQHVTIPARD-VNEEFFENGQMFDGSSIHGWKGIN 61 Query: 62 ASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGIG 121 SDMIL P+D TA LDPFTEDATL++ CDIIEP+TMQGY+RDPR+IA RAE YL++TG+G Sbjct: 62 ESDMILRPEDGTAFLDPFTEDATLVVRCDIIEPATMQGYERDPRSIAKRAEAYLQSTGLG 121 Query: 122 DTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYFP 181 DT F GPEPEFFIFD+V +K+DI G+M+KI SE+G+W +D+ +EGGN GHRP VKGGYFP Sbjct: 122 DTAFFGPEPEFFIFDQVHWKADIEGAMYKITSEEGAWSTDRQLEGGNLGHRPRVKGGYFP 181 Query: 182 VPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKYV 241 VPP D H+IR AMCN LE +GQTVEVHHHEV+ AGQNEIGVKFNTLVKKADEVQ LKYV Sbjct: 182 VPPVDSFHDIRGAMCNTLEAIGQTVEVHHHEVSNAGQNEIGVKFNTLVKKADEVQELKYV 241 Query: 242 VHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGGI 301 +HNVA AYG+TATFMPKPL GDNGSGMHVH S KDG+N FAG+ YAGLSE ALY+IGGI Sbjct: 242 IHNVAHAYGKTATFMPKPLVGDNGSGMHVHQSFWKDGQNQFAGDQYAGLSEMALYYIGGI 301 Query: 302 IKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARFP 361 IKH +ALN FTN +TNSYKRLVPGFEAPVMLAYSARNRSASIRIPY SP+G+RIEARFP Sbjct: 302 IKHARALNAFTNASTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYTASPKGKRIEARFP 361 Query: 362 DPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEEL 421 DP ANPYLAF+A+LMAG+DGI+NKIHPGDA DKNLYDLPPEE K++P V SL +ALE L Sbjct: 362 DPTANPYLAFSAMLMAGIDGIKNKIHPGDAMDKNLYDLPPEEGKKVPTVAHSLDQALEAL 421 Query: 422 DKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYSC 468 DK RAFLT+GGVF+DD IDAYI LK E+ ++R HP+E+++YYSC Sbjct: 422 DKDRAFLTEGGVFTDDMIDAYIELKMEDVERIRMTTHPIEFDMYYSC 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: 774 Number of extensions: 24 Number of successful extensions: 2 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 WP_086510693.1 BZY95_RS14880 (glutamate--ammonia ligase)
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.3524.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-210 685.7 0.0 1.7e-210 685.5 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510693.1 BZY95_RS14880 glutamate--ammonia Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510693.1 BZY95_RS14880 glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 685.5 0.0 1.7e-210 1.7e-210 3 462 .] 5 467 .. 3 467 .. 0.99 Alignments for each domain: == domain 1 score: 685.5 bits; conditional E-value: 1.7e-210 TIGR00653 3 vlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpet 71 l+l++e++vk vdlrf+D++Gk+++v+ip+++++ee++e+g +FDgss++G+k+i+esD++l p+ t lcl|NCBI__GCF_002151265.1:WP_086510693.1 5 TLALIEEHDVKWVDLRFTDTRGKEQHVTIPARDVNEEFFENGQMFDGSSIHGWKGINESDMILRPEDGT 73 567899*************************************************************** PP TIGR00653 72 lvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefke 139 ++ +Pf+++ +l+v+cd+ ep+t++ yerdpRsiakrae +l+ t+lgd+++fGpE+EFf+fd+v+ k lcl|NCBI__GCF_002151265.1:WP_086510693.1 74 AFLDPFTEDATLVVRCDIIEPATMQGYERDPRSIAKRAEAYLQsTGLGDTAFFGPEPEFFIFDQVHWKA 142 ********************************************************************* PP TIGR00653 140 asnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHH 206 + +++++ seeg+w+ r+ e+gn g++++ kggYf+v+pvD+ +dir ++++le++g +vev+HH lcl|NCBI__GCF_002151265.1:WP_086510693.1 143 DIEGAMYKITSEEGAWStdRQLEGGNLGHRPRVKGGYFPVPPVDSFHDIRGAMCNTLEAIGQTVEVHHH 211 ****************9999************************************************* PP TIGR00653 207 Evata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274 Ev++a q+Ei++kf++lvk+aDe++ +Kyv++nva+ +GktatFmpKpl+gdngsGmHvh+s wkdg+n lcl|NCBI__GCF_002151265.1:WP_086510693.1 212 EVSNAgQNEIGVKFNTLVKKADEVQELKYVIHNVAHAYGKTATFMPKPLVGDNGSGMHVHQSFWKDGQN 280 ********************************************************************* PP TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343 fag++ yagLse+alyyigGi+kHa+al+A+tn+++nsYkRLvpG+EAPv+laysa+nRsa+iRiP++ lcl|NCBI__GCF_002151265.1:WP_086510693.1 281 QFAGDQ-YAGLSEMALYYIGGIIKHARALNAFTNASTNSYKRLVPGFEAPVMLAYSARNRSASIRIPYT 348 ******.************************************************************** PP TIGR00653 344 anpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLe 412 a+pk+kRiE R+pDp+anpYLaf+a+lmAg+dGiknki+pg+++dknly+l++ee k+ ++++++sL+ lcl|NCBI__GCF_002151265.1:WP_086510693.1 349 ASPKGKRIEARFPDPTANPYLAFSAMLMAGIDGIKNKIHPGDAMDKNLYDLPPEEGKK--VPTVAHSLD 415 **********************************************************..********* PP TIGR00653 413 ealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 +al++l++d+ +++++v+++++i+a+ielk+++ve++r++ hp+E+ +y++ lcl|NCBI__GCF_002151265.1:WP_086510693.1 416 QALEALDKDRafLTEGGVFTDDMIDAYIELKMEDVERIRMTTHPIEFDMYYS 467 **********9999************************************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: 10.86 // [ok]
This GapMind analysis is from Apr 10 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