Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_028989447.1 G579_RS0105900 glutamate--ammonia ligase
Query= BRENDA::P0A1P6 (469 letters) >NCBI__GCF_000423825.1:WP_028989447.1 Length = 471 Score = 689 bits (1779), Expect = 0.0 Identities = 329/468 (70%), Positives = 383/468 (81%) Query: 2 SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGI 61 + + V ++ E++VKF+DLRFTDTKGKEQHV++PAH ++ FEEGK FDGSSI GWK I Sbjct: 4 AVKDVFKLIEENDVKFIDLRFTDTKGKEQHVSMPAHALDEGAFEEGKAFDGSSIAGWKHI 63 Query: 62 NESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATGI 121 NESDM+L D S+AV+DPF ++TLIIRCDI+EP T +GY+RDPRSIAKRAE YL++TGI Sbjct: 64 NESDMILKLDPSSAVMDPFMDENTLIIRCDIIEPATGEGYERDPRSIAKRAEAYLKSTGI 123 Query: 122 ADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGYF 181 ADT FGPE EFF+FD + + +SG ID E AWNS +YE GN HRP VKGGYF Sbjct: 124 ADTAYFGPENEFFIFDSVTWSIDMSGCSYKIDSQEAAWNSGKEYESGNMAHRPSVKGGYF 183 Query: 182 PVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKY 241 PVPPVDS+QDIRS MCL +E+MG+ VE HHHEVATA QNE+ F T+T+KADE+QI KY Sbjct: 184 PVPPVDSSQDIRSAMCLALEEMGIKVEVHHHEVATANQNEIGVAFGTLTRKADEVQILKY 243 Query: 242 VVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIGG 301 VVHNVAH +G TATFMPKP+ GDNGSGMH HMSLAK+G NLFSGD Y G+SE ALYYIGG Sbjct: 244 VVHNVAHAYGHTATFMPKPIVGDNGSGMHVHMSLAKDGKNLFSGDGYGGMSELALYYIGG 303 Query: 302 VIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVRF 361 +IKHAKA+NA+ NP+TNSYKRLVPG+EAPVMLAYSARNRSASIRIP V +PKARRIEVRF Sbjct: 304 IIKHAKALNAITNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPFVTNPKARRIEVRF 363 Query: 362 PDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNA 421 PD ANPYL FAA++MAGLDGI+NKIHPGEAMDK+LYDLP EE K IPQV GSL EAL+A Sbjct: 364 PDSTANPYLAFAAMMMAGLDGIQNKIHPGEAMDKDLYDLPAEEKKSIPQVCGSLSEALDA 423 Query: 422 LDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469 LD DR FL GGVFTD +DA+I L+R E V MT HPVE +YYS+ Sbjct: 424 LDADRAFLTKGGVFTDSMLDAFIELKRAEVQEVNMTTHPVEMRMYYSL 471 Lambda K H 0.318 0.136 0.401 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: 767 Number of extensions: 29 Number of successful extensions: 1 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: 471 Length adjustment: 33 Effective length of query: 436 Effective length of database: 438 Effective search space: 190968 Effective search space used: 190968 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_028989447.1 G579_RS0105900 (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.27318.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-212 691.4 0.1 3.1e-212 691.2 0.1 1.0 1 lcl|NCBI__GCF_000423825.1:WP_028989447.1 G579_RS0105900 glutamate--ammoni Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028989447.1 G579_RS0105900 glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 691.2 0.1 3.1e-212 3.1e-212 2 462 .] 7 470 .. 6 470 .. 0.99 Alignments for each domain: == domain 1 score: 691.2 bits; conditional E-value: 3.1e-212 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +v+kl++e++vkf+dlrf+D+kGk+++v++p+++l+e a+eeg+aFDgss+ G+k+i+esD++lk dp+ lcl|NCBI__GCF_000423825.1:WP_028989447.1 7 DVFKLIEENDVKFIDLRFTDTKGKEQHVSMPAHALDEGAFEEGKAFDGSSIAGWKHINESDMILKLDPS 75 789****************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 ++v++Pf++e++l+++cd+ ep+t+e yerdpRsiakrae +lk t+++d++yfGpE+EFf+fd+v+ + lcl|NCBI__GCF_000423825.1:WP_028989447.1 76 SAVMDPFMDENTLIIRCDIIEPATGEGYERDPRSIAKRAEAYLKsTGIADTAYFGPENEFFIFDSVTWS 144 ********************************************************************* PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 ++ +++ds+e++wn +e+e+gn +++++ kggYf+v+pvD+ +dir+ ++lalee+g++vev+H lcl|NCBI__GCF_000423825.1:WP_028989447.1 145 IDMSGCSYKIDSQEAAWNsgKEYESGNMAHRPSVKGGYFPVPPVDSSQDIRSAMCLALEEMGIKVEVHH 213 *******************9************************************************* PP TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273 HEvata q+Ei++ f +l+++aDe++++Kyvv+nva+ +G+tatFmpKp++gdngsGmHvh+sl kdg+ lcl|NCBI__GCF_000423825.1:WP_028989447.1 214 HEVATAnQNEIGVAFGTLTRKADEVQILKYVVHNVAHAYGHTATFMPKPIVGDNGSGMHVHMSLAKDGK 282 ********************************************************************* PP TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342 nlf+g+ y g+se alyyigGi+kHakal+A+tnp++nsYkRLvpG+EAPv+laysa+nRsa+iRiP lcl|NCBI__GCF_000423825.1:WP_028989447.1 283 NLFSGDG-YGGMSELALYYIGGIIKHAKALNAITNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPF 350 ******9.************************************************************* PP TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411 ++npka+RiEvR+pD++anpYLafaa++mAgldGi+nki+pge++dk+ly+l+ ee+k+ i+q+ sL lcl|NCBI__GCF_000423825.1:WP_028989447.1 351 VTNPKARRIEVRFPDSTANPYLAFAAMMMAGLDGIQNKIHPGEAMDKDLYDLPAEEKKS--IPQVCGSL 417 ***********************************************************..******** PP TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 +eald+l++d+ +++++v+++ +++afielkr+Ev+e++++ hpvE+ +y++ lcl|NCBI__GCF_000423825.1:WP_028989447.1 418 SEALDALDADRafLTKGGVFTDSMLDAFIELKRAEVQEVNMTTHPVEMRMYYS 470 ***********9999************************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.23 // [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