Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate CCNA_02047 CCNA_02047 glutamine synthetase
Query= CharProtDB::CH_024014 (469 letters) >FitnessBrowser__Caulo:CCNA_02047 Length = 469 Score = 600 bits (1547), Expect = e-176 Identities = 292/466 (62%), Positives = 355/466 (76%), Gaps = 1/466 (0%) Query: 2 SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGI 61 +A+ +L ++ E +VK+VD+RFTD +GK QHVT V+ +F +G MFDGSSI GWK I Sbjct: 3 TAKDILNLIKEKDVKYVDVRFTDVRGKMQHVTFDIDLVDDDFLNDGTMFDGSSIAGWKAI 62 Query: 62 NESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTGI 121 NESDM L PD S+A+IDPF+ +TL + CD++ P T Y+RDPRSIAK A +YL+S G+ Sbjct: 63 NESDMKLRPDLSSAIIDPFYQQTTLALFCDVVNPDTGTPYNRDPRSIAKAALNYLKSAGV 122 Query: 122 ADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGYF 181 DTV FGPE EFF+FDD+R+ ++ + + D E NS+ QY GN GHRP KGGYF Sbjct: 123 GDTVYFGPEAEFFIFDDVRWSTAPHDTSYSFDSTELPVNSNKQYAEGNMGHRPGPKGGYF 182 Query: 182 PVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKY 241 PV PVDS QD+R EM VM ++G+ E HHHEVA A Q+E+ +F+TM AD +Q+YKY Sbjct: 183 PVNPVDSCQDLRGEMLAVMGELGMKPEKHHHEVAPA-QHELGLKFDTMVTMADRMQLYKY 241 Query: 242 VVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIGG 301 V+HNVA +GKTATFM KPMF DNGSGMH H S+ ++G LFAGDKYAGLS++ L+YIGG Sbjct: 242 VIHNVAAAYGKTATFMAKPMFADNGSGMHVHQSIWQDGKPLFAGDKYAGLSQECLWYIGG 301 Query: 302 VIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVRF 361 +IKHAKAINA +N TTNSYKRLVPGYEAPV LAYS+RNRSASIRIP V SPKA+R+E RF Sbjct: 302 IIKHAKAINAFSNSTTNSYKRLVPGYEAPVKLAYSSRNRSASIRIPHVDSPKAKRLEARF 361 Query: 362 PDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNE 421 PDP NPYL F ALLMAGLDGI NKI PG DKNLYDLPP E K+IP+V GSL EAL Sbjct: 362 PDPMGNPYLTFVALLMAGLDGIINKIDPGAPADKNLYDLPPREQKKIPEVCGSLREALEN 421 Query: 422 LDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYY 467 LD DR FLKAGGV D+ ID+YI L+ EE R+++ PHPVEFE+YY Sbjct: 422 LDKDRAFLKAGGVMDDDFIDSYIELKMEEVMRLQLHPHPVEFEMYY 467 Lambda K H 0.318 0.136 0.400 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: 721 Number of extensions: 34 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: 469 Length of database: 469 Length adjustment: 33 Effective length of query: 436 Effective length of database: 436 Effective search space: 190096 Effective search space used: 190096 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 CCNA_02047 CCNA_02047 (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.13107.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-199 646.8 0.0 1e-198 646.6 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_02047 CCNA_02047 glutamine synthetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_02047 CCNA_02047 glutamine synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 646.6 0.0 1e-198 1e-198 2 462 .] 6 468 .. 5 468 .. 0.99 Alignments for each domain: == domain 1 score: 646.6 bits; conditional E-value: 1e-198 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpetlvi 74 ++l+l+ke++vk+vd+rf+D++Gk+++v++ ++ +++++l++g++FDgss+ G+k+i+esD+ l pd+++++i lcl|FitnessBrowser__Caulo:CCNA_02047 6 DILNLIKEKDVKYVDVRFTDVRGKMQHVTFDIDLVDDDFLNDGTMFDGSSIAGWKAINESDMKLRPDLSSAII 78 68899******************************************************************** PP TIGR00653 75 vPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefkeasnssfl 146 +Pf ++++l ++cdv +p t++py+rdpRsiak a+++lk +++gd+vyfGpEaEFf+fd+v+ ++a +++ + lcl|FitnessBrowser__Caulo:CCNA_02047 79 DPFYQQTTLALFCDVVNPDTGTPYNRDPRSIAKAALNYLKsAGVGDTVYFGPEAEFFIFDDVRWSTAPHDTSY 151 ****************************************99******************************* PP TIGR00653 147 evdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsHHEvataqaEidi 217 + ds+e n +++ egn g+++ kggYf+v+pvD+ +d+r e++ ++ elg++ e++HHEva+aq+E+++ lcl|FitnessBrowser__Caulo:CCNA_02047 152 SFDSTELPVNsnKQYAEGNMGHRPGPKGGYFPVNPVDSCQDLRGEMLAVMGELGMKPEKHHHEVAPAQHELGL 224 *****988776699999******************************************************** PP TIGR00653 218 kfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgenlfageegyagLsetal 290 kfd++v++aD ++lyKyv++nva+ +GktatFm+Kp+f dngsGmHvh+s+w+dg++lfag++ yagLs+++l lcl|FitnessBrowser__Caulo:CCNA_02047 225 KFDTMVTMADRMQLYKYVIHNVAAAYGKTATFMAKPMFADNGSGMHVHQSIWQDGKPLFAGDK-YAGLSQECL 296 ***************************************************************.********* PP TIGR00653 291 yyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPasanpkakRiEvRspDpsanpY 363 +yigGi+kHaka++A+ n+t+nsYkRLvpGyEAPv+lays +nRsa+iRiP + +pkakR+E R+pDp +npY lcl|FitnessBrowser__Caulo:CCNA_02047 297 WYIGGIIKHAKAINAFSNSTTNSYKRLVPGYEAPVKLAYSSRNRSASIRIPHVDSPKAKRLEARFPDPMGNPY 369 ************************************************************************* PP TIGR00653 364 LafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLeealdelesdk..evlkevlgeeli 434 L+f allmAgldGi nkidpg+p dknly+l++ e+k+ i+++ sL+eal++l++d+ +++++v+ +++i lcl|FitnessBrowser__Caulo:CCNA_02047 370 LTFVALLMAGLDGIINKIDPGAPADKNLYDLPPREQKK--IPEVCGSLREALENLDKDRafLKAGGVMDDDFI 440 **************************************..*******************999999******** PP TIGR00653 435 eafielkrkEveelrlkvhpvElekyld 462 +++ielk++Ev +l+l++hpvE+e+y++ lcl|FitnessBrowser__Caulo:CCNA_02047 441 DSYIELKMEEVMRLQLHPHPVEFEMYYK 468 **************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (469 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: 9.90 // [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