Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate WP_012400875.1 BPHY_RS07555 type I glutamate--ammonia ligase
Query= SwissProt::Q3V5W6 (468 letters) >NCBI__GCF_000020045.1:WP_012400875.1 Length = 471 Score = 658 bits (1698), Expect = 0.0 Identities = 317/471 (67%), Positives = 377/471 (80%), Gaps = 5/471 (1%) Query: 1 MSKSV----QLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAG 56 MSKSV QL+KD DVK++D RFTDT+G + HV++P A ++D FE G FDGSSIAG Sbjct: 1 MSKSVADVMQLVKDEDVKFVDFRFTDTRGKEQHVSVPV-SAFDEDKFESGHAFDGSSIAG 59 Query: 57 WKGIEASDMILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLK 116 WKGIEASDM+L+PD +TA +DPF E++TL+L CD++EP+ +GY+RDPR++A RAE YLK Sbjct: 60 WKGIEASDMLLVPDSNTAFIDPFYEESTLVLTCDVVEPADGKGYERDPRSLAKRAEAYLK 119 Query: 117 TTGIGDTVFAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVK 176 +TG+GDT F GPEPEFFIFD V++ +D SG KI SE+ W S ++ EGGN GHRPG K Sbjct: 120 STGLGDTAFFGPEPEFFIFDSVQWNTDQSGCFVKIGSEEAPWSSGKEFEGGNTGHRPGTK 179 Query: 177 GGYFPVPPFDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQ 236 GGYFPV P D +IR+ MC LE++G VEVHHHEVA GQNEIG KF+TLV++AD Q Sbjct: 180 GGYFPVAPVDTFQDIRSEMCLLLEQIGIPVEVHHHEVAGQGQNEIGTKFSTLVQRADWTQ 239 Query: 237 TLKYVVHNVADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALY 296 LKY+VHNVA YG+TATFMPKP+ GDNGSGMHVH SI KDG+N FAG GYAGLSE AL+ Sbjct: 240 QLKYIVHNVAHTYGKTATFMPKPVVGDNGSGMHVHQSIWKDGQNMFAGNGYAGLSEFALF 299 Query: 297 FIGGIIKHGKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRI 356 +IGGIIKH +ALN TNP TNSYKRLVP FEAPV LAYSARNRSASIRIP+V +P+GRRI Sbjct: 300 YIGGIIKHARALNAITNPGTNSYKRLVPHFEAPVKLAYSARNRSASIRIPHVANPKGRRI 359 Query: 357 EARFPDPAANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKE 416 E RFPDP ANPYL F+AL+MAGLDG+QNKIHPG+AADKNLYDLPPEE +IP VC L + Sbjct: 360 ETRFPDPLANPYLCFSALMMAGLDGVQNKIHPGEAADKNLYDLPPEEDAKIPTVCAGLDQ 419 Query: 417 ALEELDKGRAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYS 467 ALE LD R FLT+GGVF+D IDAY+ LK E +VR HP+E+ELYYS Sbjct: 420 ALEALDADREFLTRGGVFTDGMIDAYLELKESELQRVRMTTHPVEFELYYS 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: 789 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: 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_012400875.1 BPHY_RS07555 (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.6404.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-203 661.8 0.0 3e-203 661.6 0.0 1.0 1 lcl|NCBI__GCF_000020045.1:WP_012400875.1 BPHY_RS07555 type I glutamate--a Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020045.1:WP_012400875.1 BPHY_RS07555 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 661.6 0.0 3e-203 3e-203 2 462 .] 7 470 .. 6 470 .. 0.99 Alignments for each domain: == domain 1 score: 661.6 bits; conditional E-value: 3e-203 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +v++l+k+e+vkfvd+rf+D++Gk+++v++pvs+++e+ +e+g aFDgss+ G+k+ie sD+ll+pd + lcl|NCBI__GCF_000020045.1:WP_012400875.1 7 DVMQLVKDEDVKFVDFRFTDTRGKEQHVSVPVSAFDEDKFESGHAFDGSSIAGWKGIEASDMLLVPDSN 75 6899***************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 t++i+Pf +e++l+++cdv ep++++ yerdpRs akrae +lk t+lgd+++fGpE+EFf+fd+v+ + lcl|NCBI__GCF_000020045.1:WP_012400875.1 76 TAFIDPFYEESTLVLTCDVVEPADGKGYERDPRSLAKRAEAYLKsTGLGDTAFFGPEPEFFIFDSVQWN 144 ********************************************************************* PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 + ++ f+++ see+ w+ +e+e+gn+g+++ +kggYf+v+pvD+ +dir+e++l le++g+ vev+H lcl|NCBI__GCF_000020045.1:WP_012400875.1 145 TDQSGCFVKIGSEEAPWSsgKEFEGGNTGHRPGTKGGYFPVAPVDTFQDIRSEMCLLLEQIGIPVEVHH 213 *****************999************************************************* PP TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273 HEva q+Ei++kf++lv+ aD ++++Ky+v+nva+ +GktatFmpKp++gdngsGmHvh+s+wkdg+ lcl|NCBI__GCF_000020045.1:WP_012400875.1 214 HEVAGQgQNEIGTKFSTLVQRADWTQQLKYIVHNVAHTYGKTATFMPKPVVGDNGSGMHVHQSIWKDGQ 282 ***9666************************************************************** PP TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342 n+fag+ yagLse al+yigGi+kHa+al+A+tnp +nsYkRLvp +EAPv+laysa+nRsa+iRiP lcl|NCBI__GCF_000020045.1:WP_012400875.1 283 NMFAGNG-YAGLSEFALFYIGGIIKHARALNAITNPGTNSYKRLVPHFEAPVKLAYSARNRSASIRIPH 350 ******9.************************************************************* PP TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411 +anpk++RiE R+pDp anpYL+f+al+mAgldG++nki+pge+ dknly+l++ee ++ i+++ + L lcl|NCBI__GCF_000020045.1:WP_012400875.1 351 VANPKGRRIETRFPDPLANPYLCFSALMMAGLDGVQNKIHPGEAADKNLYDLPPEEDAK--IPTVCAGL 417 ***********************************************************..******** PP TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 ++al++l++d+ ++ ++v+++ +i+a++elk++E +++r++ hpvE+e y++ lcl|NCBI__GCF_000020045.1:WP_012400875.1 418 DQALEALDADRefLTRGGVFTDGMIDAYLELKESELQRVRMTTHPVEFELYYS 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: 9.44 // [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