Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate WP_029000178.1 H537_RS0125925 type I glutamate--ammonia ligase
Query= SwissProt::Q3V5W6 (468 letters) >NCBI__GCF_000430725.1:WP_029000178.1 Length = 471 Score = 640 bits (1651), Expect = 0.0 Identities = 299/463 (64%), Positives = 376/463 (81%), Gaps = 1/463 (0%) Query: 5 VQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGIEASD 64 ++++K+++VK++D RFTDT+G + HV++P ++D F+ G FDGSSIAGWKGIEASD Sbjct: 9 MKIVKENEVKFVDFRFTDTRGKEQHVSVPVSH-FDEDKFQSGHAFDGSSIAGWKGIEASD 67 Query: 65 MILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGIGDTV 124 M+L+PD +TA +DPF E+ TLIL CD+I+P+ + Y+RDPR++A RAE Y++ +G+GDT Sbjct: 68 MLLMPDPNTANIDPFFEEPTLILTCDVIDPADGKPYERDPRSLAKRAEAYMRASGLGDTA 127 Query: 125 FAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYFPVPP 184 F GPEPEFF+FD V++ D+SG KI SE+ +W + ++ E GN G RP VKGGYFPVPP Sbjct: 128 FFGPEPEFFVFDSVRWNIDMSGCFSKIESEEAAWNTGKEYEHGNSGFRPSVKGGYFPVPP 187 Query: 185 FDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKYVVHN 244 D ++R+ MC LE++G VEVHHHEVATAGQ EIG KF+TL+++AD VQ KYV+HN Sbjct: 188 VDSGQDLRSEMCLLLEQLGIPVEVHHHEVATAGQMEIGTKFSTLIERADWVQLQKYVIHN 247 Query: 245 VADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGGIIKH 304 VA AYG+TATFMPKP+ GDNGSGMHVH S+ KDGKN FAG+GYAGLS+ ALY+IGGIIKH Sbjct: 248 VAAAYGKTATFMPKPIVGDNGSGMHVHQSVWKDGKNLFAGDGYAGLSDFALYYIGGIIKH 307 Query: 305 GKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARFPDPA 364 +ALN TNP TNSYKRLVPGFEAPV LAYSA+NRSASIRIPYV +P+GRR+EARFPDP Sbjct: 308 ARALNAITNPGTNSYKRLVPGFEAPVKLAYSAKNRSASIRIPYVANPKGRRVEARFPDPL 367 Query: 365 ANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEELDKG 424 NPYL FAALLMAGLDG++NKIHPG+AA K+LY LPPEE +IP VC SL +ALE LDK Sbjct: 368 MNPYLGFAALLMAGLDGVENKIHPGEAATKDLYHLPPEEDAKIPTVCHSLDQALEALDKD 427 Query: 425 RAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYS 467 RAFLTKGGVF+D +IDAYI LK +E + R HP+E+++YY+ Sbjct: 428 RAFLTKGGVFTDSYIDAYIDLKMQEVTRFRMATHPVEFDMYYA 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: 762 Number of extensions: 36 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 WP_029000178.1 H537_RS0125925 (type I 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.9190.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-206 671.0 0.0 4.6e-206 670.9 0.0 1.0 1 lcl|NCBI__GCF_000430725.1:WP_029000178.1 H537_RS0125925 type I glutamate- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_029000178.1 H537_RS0125925 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 670.9 0.0 4.6e-206 4.6e-206 2 461 .. 7 469 .. 6 470 .. 0.99 Alignments for each domain: == domain 1 score: 670.9 bits; conditional E-value: 4.6e-206 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +v+k++ke++vkfvd+rf+D++Gk+++v++pvs+++e+ +++g aFDgss+ G+k+ie sD+ll+pdp+ lcl|NCBI__GCF_000430725.1:WP_029000178.1 7 DVMKIVKENEVKFVDFRFTDTRGKEQHVSVPVSHFDEDKFQSGHAFDGSSIAGWKGIEASDMLLMPDPN 75 6899***************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 t+ i+Pf +e++l+++cdv +p++++pyerdpRs akrae +++ ++lgd+++fGpE+EFf+fd+v+ + lcl|NCBI__GCF_000430725.1:WP_029000178.1 76 TANIDPFFEEPTLILTCDVIDPADGKPYERDPRSLAKRAEAYMRaSGLGDTAFFGPEPEFFVFDSVRWN 144 ********************************************9************************ PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 ++ f +++see++wn +e+e+gn+g++++ kggYf+v+pvD+ +d+r+e++l le+lg+ vev+H lcl|NCBI__GCF_000430725.1:WP_029000178.1 145 IDMSGCFSKIESEEAAWNtgKEYEHGNSGFRPSVKGGYFPVPPVDSGQDLRSEMCLLLEQLGIPVEVHH 213 ******************999************************************************ PP TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273 HEvata q Ei++kf++l++ aD ++l Kyv++nva+ +GktatFmpKp++gdngsGmHvh+s+wkdg+ lcl|NCBI__GCF_000430725.1:WP_029000178.1 214 HEVATAgQMEIGTKFSTLIERADWVQLQKYVIHNVAAAYGKTATFMPKPIVGDNGSGMHVHQSVWKDGK 282 ********************************************************************* PP TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342 nlfag+ yagLs+ alyyigGi+kHa+al+A+tnp +nsYkRLvpG+EAPv+laysaknRsa+iRiP+ lcl|NCBI__GCF_000430725.1:WP_029000178.1 283 NLFAGDG-YAGLSDFALYYIGGIIKHARALNAITNPGTNSYKRLVPGFEAPVKLAYSAKNRSASIRIPY 350 ******9.************************************************************* PP TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411 +anpk++R+E R+pDp npYL faallmAgldG++nki+pge+ k+ly+l++ee ++ i+++ +sL lcl|NCBI__GCF_000430725.1:WP_029000178.1 351 VANPKGRRVEARFPDPLMNPYLGFAALLMAGLDGVENKIHPGEAATKDLYHLPPEEDAK--IPTVCHSL 417 ***********************************************************..******** PP TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyl 461 ++al++l++d+ +++++v+++ i+a+i+lk++Ev ++r++ hpvE+ +y+ lcl|NCBI__GCF_000430725.1:WP_029000178.1 418 DQALEALDKDRafLTKGGVFTDSYIDAYIDLKMQEVTRFRMATHPVEFDMYY 469 ***********9999************************************9 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 10.82 // [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