Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate WP_028312523.1 H566_RS0117970 glutamate--ammonia ligase
Query= CharProtDB::CH_024014 (469 letters) >NCBI__GCF_000482785.1:WP_028312523.1 Length = 471 Score = 675 bits (1742), Expect = 0.0 Identities = 323/469 (68%), Positives = 385/469 (82%) Query: 1 MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60 ++A+ V+ ++ ++EVKFVD RFTDTKGKEQHV++P + + FE G FDGSSI GWKG Sbjct: 3 ITADDVMKLVKDNEVKFVDFRFTDTKGKEQHVSVPLSHFDKDKFESGHAFDGSSIAGWKG 62 Query: 61 INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTG 120 I SDM+LMPDA+TA IDPF ++TLI+ CD+LEP +GYDRDPRSIAKRAE YL+S+G Sbjct: 63 IEASDMLLMPDANTAFIDPFREETTLILTCDVLEPSDGKGYDRDPRSIAKRAEAYLKSSG 122 Query: 121 IADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGY 180 I DT FGPEPEFF+FD +R+G+ +SGS V I+ E +W++ +YEGGN HRPAVKGGY Sbjct: 123 IGDTAFFGPEPEFFIFDGVRWGADMSGSFVEIESEEASWSTGKKYEGGNLAHRPAVKGGY 182 Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240 FPVPPVDS QDIRSEMCL++EQ+G+ VE HHHEVA AGQNE+ T+F+T+ ++AD Q K Sbjct: 183 FPVPPVDSFQDIRSEMCLILEQIGVPVEVHHHEVAGAGQNEIGTKFSTLVERADWTQKLK 242 Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIG 300 YVVHNVA +GKTATFMPKP+ GDNGSGMH H S+ K+G NLFAGD YAGLSE ALYYIG Sbjct: 243 YVVHNVAASYGKTATFMPKPLVGDNGSGMHVHQSVWKDGKNLFAGDGYAGLSEFALYYIG 302 Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVR 360 G+IKHA+A+NA+ NP TNSYKRLVPG+EAPV LAYSARNRSASIRIP V+S KARRIEVR Sbjct: 303 GIIKHARALNAITNPGTNSYKRLVPGFEAPVKLAYSARNRSASIRIPYVNSDKARRIEVR 362 Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420 FPDP AN YL FAA+LMAGLDG++NKIHPGEA DKNLYDLPPEE IP V SL++AL Sbjct: 363 FPDPTANSYLAFAAMLMAGLDGVQNKIHPGEAADKNLYDLPPEEDALIPTVCSSLDQALE 422 Query: 421 ELDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469 LD DREFL GGVFTD IDAYIAL+ E+ R RMT HP+EF++YYS+ Sbjct: 423 YLDKDREFLTKGGVFTDSMIDAYIALKMEDVTRFRMTTHPIEFDMYYSL 471 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: 741 Number of extensions: 28 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_028312523.1 H566_RS0117970 (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.23671.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-209 680.8 0.0 4.9e-209 680.7 0.0 1.0 1 lcl|NCBI__GCF_000482785.1:WP_028312523.1 H566_RS0117970 glutamate--ammoni Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000482785.1:WP_028312523.1 H566_RS0117970 glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 680.7 0.0 4.9e-209 4.9e-209 2 462 .] 7 470 .. 6 470 .. 0.99 Alignments for each domain: == domain 1 score: 680.7 bits; conditional E-value: 4.9e-209 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +v+kl+k+++vkfvd+rf+D+kGk+++v++p+s+++++ +e+g aFDgss+ G+k+ie sD+ll+pd++ lcl|NCBI__GCF_000482785.1:WP_028312523.1 7 DVMKLVKDNEVKFVDFRFTDTKGKEQHVSVPLSHFDKDKFESGHAFDGSSIAGWKGIEASDMLLMPDAN 75 7899***************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 t++i+Pfr+e++l+++cdv ep +++ y+rdpRsiakrae +lk +++gd+++fGpE+EFf+fd v+ + lcl|NCBI__GCF_000482785.1:WP_028312523.1 76 TAFIDPFREETTLILTCDVLEPSDGKGYDRDPRSIAKRAEAYLKsSGIGDTAFFGPEPEFFIFDGVRWG 144 ********************************************99*********************** PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 ++ sf+e++see++w+ +++e+gn +++++ kggYf+v+pvD+ +dir+e++l+le++g+ vev+H lcl|NCBI__GCF_000482785.1:WP_028312523.1 145 ADMSGSFVEIESEEASWStgKKYEGGNLAHRPAVKGGYFPVPPVDSFQDIRSEMCLILEQIGVPVEVHH 213 *****************9999************************************************ PP TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273 HEva a q+Ei++kf++lv+ aD ++++Kyvv+nva+ +GktatFmpKpl+gdngsGmHvh+s+wkdg+ lcl|NCBI__GCF_000482785.1:WP_028312523.1 214 HEVAGAgQNEIGTKFSTLVERADWTQKLKYVVHNVAASYGKTATFMPKPLVGDNGSGMHVHQSVWKDGK 282 ****999************************************************************** PP TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342 nlfag+ yagLse alyyigGi+kHa+al+A+tnp +nsYkRLvpG+EAPv+laysa+nRsa+iRiP+ lcl|NCBI__GCF_000482785.1:WP_028312523.1 283 NLFAGDG-YAGLSEFALYYIGGIIKHARALNAITNPGTNSYKRLVPGFEAPVKLAYSARNRSASIRIPY 350 ******9.************************************************************* PP TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411 + + ka+RiEvR+pDp+an+YLafaa+lmAgldG++nki+pge+ dknly+l++ee + i+++ +sL lcl|NCBI__GCF_000482785.1:WP_028312523.1 351 VNSDKARRIEVRFPDPTANSYLAFAAMLMAGLDGVQNKIHPGEAADKNLYDLPPEEDAL--IPTVCSSL 417 ********************************************************999..******** PP TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 ++al+ l++d+ +++++v+++ +i+a+i+lk+++v ++r++ hp+E+ +y++ lcl|NCBI__GCF_000482785.1:WP_028312523.1 418 DQALEYLDKDRefLTKGGVFTDSMIDAYIALKMEDVTRFRMTTHPIEFDMYYS 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12.27 // [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