Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_057509241.1 ABB28_RS14190 type I glutamate--ammonia ligase
Query= BRENDA::P0A1P6 (469 letters) >NCBI__GCF_001431535.1:WP_057509241.1 Length = 469 Score = 639 bits (1647), Expect = 0.0 Identities = 302/468 (64%), Positives = 367/468 (78%) Query: 1 MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60 MS E+V ++ +++++FVDLRF D +G EQHVT P + A FEEGKMFDGSSI GWKG Sbjct: 1 MSVENVEKLVKDNQIEFVDLRFVDMRGIEQHVTFPVSIIEASLFEEGKMFDGSSIAGWKG 60 Query: 61 INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATG 120 INESDMVL+PD S+A +DPF+AD T++I CDIL+P T+Q Y R PR IAKRAE +L+++G Sbjct: 61 INESDMVLLPDPSSAYVDPFYADPTIVISCDILDPATMQPYGRCPRGIAKRAEAFLKSSG 120 Query: 121 IADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGY 180 IA+ FGPEPEFF+FD +RF + + +D E AWN+ KY+G N G+RPGVKGGY Sbjct: 121 IAEQAFFGPEPEFFIFDSVRFANDMGNTFFKVDSEEAAWNTGAKYDGANSGYRPGVKGGY 180 Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240 FPVPP DS D+R+EMC +EQ+G+ VE HHEVATAGQ E+ T+F+T+ +KADE+ K Sbjct: 181 FPVPPTDSLHDLRAEMCKTLEQVGIEVEVQHHEVATAGQCEIGTKFSTLVQKADELLRMK 240 Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIG 300 YV+ NVAHR GKTATFMPKP+ GDNGSGMH H SL+K GTNLFSGD Y GLS+ AL+YIG Sbjct: 241 YVIKNVAHRNGKTATFMPKPIVGDNGSGMHVHQSLSKGGTNLFSGDGYGGLSQLALWYIG 300 Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVR 360 G+ KHAKAINA AN TNSYKRLVPG+EAPVMLAYSARNRSAS RIP V +PKARRIE+R Sbjct: 301 GIFKHAKAINAFANAGTNSYKRLVPGFEAPVMLAYSARNRSASCRIPFVTNPKARRIEMR 360 Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420 FPDP + YL F L+MAGLDGIKN+I PG DK+LYDLPPEE K IPQV SL++AL Sbjct: 361 FPDPIQSGYLTFTVLMMAGLDGIKNQIDPGAPSDKDLYDLPPEEEKLIPQVCSSLDQALE 420 Query: 421 ALDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYS 468 ALD DREFLKAGGV D+ ID YIAL+ +E + R HP+E++LYY+ Sbjct: 421 ALDKDREFLKAGGVMDDDFIDGYIALKMQEVTKFRAATHPLEYQLYYA 468 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: 743 Number of extensions: 27 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: 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 WP_057509241.1 ABB28_RS14190 (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.3104.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-198 644.1 0.0 6.7e-198 643.9 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509241.1 ABB28_RS14190 type I glutamate-- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057509241.1 ABB28_RS14190 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 643.9 0.0 6.7e-198 6.7e-198 1 461 [. 4 467 .. 4 468 .. 0.99 Alignments for each domain: == domain 1 score: 643.9 bits; conditional E-value: 6.7e-198 TIGR00653 1 eevlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdp 69 e+v+kl+k+++++fvdlrfvD++G++++v++pvs +e++++eeg++FDgss+ G+k+i+esD++l pdp lcl|NCBI__GCF_001431535.1:WP_057509241.1 4 ENVEKLVKDNQIEFVDLRFVDMRGIEQHVTFPVSIIEASLFEEGKMFDGSSIAGWKGINESDMVLLPDP 72 57999**************************************************************** PP TIGR00653 70 etlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvef 137 +++ ++Pf a++++++ cd+ +p+t++py r+pR iakrae lk ++++++++fGpE+EFf+fd+v+f lcl|NCBI__GCF_001431535.1:WP_057509241.1 73 SSAYVDPFYADPTIVISCDILDPATMQPYGRCPRGIAKRAEAFLKsSGIAEQAFFGPEPEFFIFDSVRF 141 *********************************************99********************** PP TIGR00653 138 keasnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevs 204 + + ++f++vdsee++wn ++++++n+gy++ kggYf+v+p+D+++d+r e++++le++g+evev+ lcl|NCBI__GCF_001431535.1:WP_057509241.1 142 ANDMGNTFFKVDSEEAAWNtgAKYDGANSGYRPGVKGGYFPVPPTDSLHDLRAEMCKTLEQVGIEVEVQ 210 *******************98899999****************************************** PP TIGR00653 205 HHEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdg 272 HHEvata q Ei++kf++lv++aDe++ +Kyv+knva+++GktatFmpKp++gdngsGmHvh+sl+k g lcl|NCBI__GCF_001431535.1:WP_057509241.1 211 HHEVATAgQCEIGTKFSTLVQKADELLRMKYVIKNVAHRNGKTATFMPKPIVGDNGSGMHVHQSLSKGG 279 ********************************************************************* PP TIGR00653 273 enlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiP 341 nlf+g+ y gLs+ al+yigGi kHaka++A++n+ +nsYkRLvpG+EAPv+laysa+nRsa+ RiP lcl|NCBI__GCF_001431535.1:WP_057509241.1 280 TNLFSGDG-YGGLSQLALWYIGGIFKHAKAINAFANAGTNSYKRLVPGFEAPVMLAYSARNRSASCRIP 347 *******9.************************************************************ PP TIGR00653 342 asanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpes 410 ++npka+RiE+R+pDp YL+f++l+mAgldGikn+idpg+p dk+ly+l++ee k i+q+ +s lcl|NCBI__GCF_001431535.1:WP_057509241.1 348 FVTNPKARRIEMRFPDPIQSGYLTFTVLMMAGLDGIKNQIDPGAPSDKDLYDLPPEEEKL--IPQVCSS 414 *********************************************************999..******* PP TIGR00653 411 Leealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyl 461 L++al++l++d+ +++++v+ +++i+ +i+lk++Ev ++r + hp+E + y+ lcl|NCBI__GCF_001431535.1:WP_057509241.1 415 LDQALEALDKDRefLKAGGVMDDDFIDGYIALKMQEVTKFRAATHPLEYQLYY 467 ************888899**********************************9 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 10.79 // [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