Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate RR42_RS12995 RR42_RS12995 glutamine synthetase
Query= SwissProt::Q3V5W6 (468 letters) >FitnessBrowser__Cup4G11:RR42_RS12995 Length = 471 Score = 650 bits (1677), Expect = 0.0 Identities = 312/463 (67%), Positives = 368/463 (79%), Gaps = 1/463 (0%) Query: 5 VQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGIEASD 64 ++L+K++DVK++D RFTDTKG + HV++P ++D FE G FDGSSIAGWKGIEASD Sbjct: 9 MKLVKENDVKFVDFRFTDTKGKEQHVSVPVSH-FDEDKFESGHAFDGSSIAGWKGIEASD 67 Query: 65 MILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGIGDTV 124 M+L+PD +TA +DPF E+ TLIL CD++EPS +GYDRDPR+IA RAE YLK+TG+GDT Sbjct: 68 MLLMPDPNTANVDPFYEEPTLILTCDVVEPSDGKGYDRDPRSIAKRAEAYLKSTGLGDTA 127 Query: 125 FAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYFPVPP 184 F GPEPEFFIFD V + D+ G KI+SE+ W S ++ E GN GHRPG KGGYFPV P Sbjct: 128 FFGPEPEFFIFDGVTWNIDMQGCSVKIHSEEAPWSSGKEFEHGNSGHRPGKKGGYFPVAP 187 Query: 185 FDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKYVVHN 244 D +IR+ MC LE +G VEVHHHEVA GQNEIG KF+TLV++AD Q KYV+ N Sbjct: 188 IDTFQDIRSEMCLILESLGIPVEVHHHEVAGQGQNEIGTKFSTLVQRADWTQLQKYVIQN 247 Query: 245 VADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGGIIKH 304 VA YG+TATFMPKP+ GDNGSGMHVH S+ KDG+N FAG GYAGLSE ALY+IGGIIKH Sbjct: 248 VAHTYGKTATFMPKPVVGDNGSGMHVHQSVWKDGQNLFAGNGYAGLSEFALYYIGGIIKH 307 Query: 305 GKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARFPDPA 364 +ALN TNP TNSYKRLVPGFEAPV LAYSARNRSASIRIPYV +P+GRRIE RFPDP Sbjct: 308 ARALNALTNPGTNSYKRLVPGFEAPVKLAYSARNRSASIRIPYVANPKGRRIETRFPDPL 367 Query: 365 ANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEELDKG 424 NPYL F+ALLMAGLDG+QNKIHPG+AADKNLYDLPPEE +IP VC SL +ALE LD Sbjct: 368 MNPYLGFSALLMAGLDGVQNKIHPGEAADKNLYDLPPEEDAKIPTVCSSLDQALEYLDND 427 Query: 425 RAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYS 467 R FLT+GGVFS+ IDAYI LK EE + R HP+E+++YYS Sbjct: 428 REFLTRGGVFSNSMIDAYIELKMEEVTRFRMTTHPIEFDMYYS 470 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: 772 Number of extensions: 27 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: 471 Length adjustment: 33 Effective length of query: 435 Effective length of database: 438 Effective search space: 190530 Effective search space used: 190530 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 RR42_RS12995 RR42_RS12995 (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.25054.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-205 668.9 0.0 2.1e-205 668.7 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS12995 RR42_RS12995 glutamine synthetas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS12995 RR42_RS12995 glutamine synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 668.7 0.0 2.1e-205 2.1e-205 2 462 .] 7 470 .. 6 470 .. 0.99 Alignments for each domain: == domain 1 score: 668.7 bits; conditional E-value: 2.1e-205 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +v+kl+ke++vkfvd+rf+D+kGk+++v++pvs+++e+ +e+g aFDgss+ G+k+ie sD+ll+pdp+ lcl|FitnessBrowser__Cup4G11:RR42_RS12995 7 DVMKLVKENDVKFVDFRFTDTKGKEQHVSVPVSHFDEDKFESGHAFDGSSIAGWKGIEASDMLLMPDPN 75 6899***************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 t+ ++Pf +e++l+++cdv ep +++ y+rdpRsiakrae +lk t+lgd+++fGpE+EFf+fd v+ + lcl|FitnessBrowser__Cup4G11:RR42_RS12995 76 TANVDPFYEEPTLILTCDVVEPSDGKGYDRDPRSIAKRAEAYLKsTGLGDTAFFGPEPEFFIFDGVTWN 144 ********************************************************************* PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 ++ ++++see+ w+ +e+e+gn+g+++ kkggYf+v+p+D+ +dir+e++l+le+lg+ vev+H lcl|FitnessBrowser__Cup4G11:RR42_RS12995 145 IDMQGCSVKIHSEEAPWSsgKEFEHGNSGHRPGKKGGYFPVAPIDTFQDIRSEMCLILESLGIPVEVHH 213 *****************999************************************************* PP TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273 HEva q+Ei++kf++lv+ aD ++l Kyv++nva+ +GktatFmpKp++gdngsGmHvh+s+wkdg+ lcl|FitnessBrowser__Cup4G11:RR42_RS12995 214 HEVAGQgQNEIGTKFSTLVQRADWTQLQKYVIQNVAHTYGKTATFMPKPVVGDNGSGMHVHQSVWKDGQ 282 ***9666************************************************************** PP TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342 nlfag+ yagLse alyyigGi+kHa+al+Altnp +nsYkRLvpG+EAPv+laysa+nRsa+iRiP+ lcl|FitnessBrowser__Cup4G11:RR42_RS12995 283 NLFAGNG-YAGLSEFALYYIGGIIKHARALNALTNPGTNSYKRLVPGFEAPVKLAYSARNRSASIRIPY 350 ******9.************************************************************* PP TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411 +anpk++RiE R+pDp npYL f+allmAgldG++nki+pge+ dknly+l++ee ++ i+++ +sL lcl|FitnessBrowser__Cup4G11:RR42_RS12995 351 VANPKGRRIETRFPDPLMNPYLGFSALLMAGLDGVQNKIHPGEAADKNLYDLPPEEDAK--IPTVCSSL 417 ***********************************************************..******** PP TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 ++al+ l++d+ ++ ++v+++ +i+a+ielk++Ev ++r++ hp+E+ +y++ lcl|FitnessBrowser__Cup4G11:RR42_RS12995 418 DQALEYLDNDRefLTRGGVFSNSMIDAYIELKMEEVTRFRMTTHPIEFDMYYS 470 ***********888999**********************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (471 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: 9.41 // [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