Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate WP_006746339.1 THITH_RS01240 glutamate--ammonia ligase
Query= CharProtDB::CH_024014 (469 letters) >NCBI__GCF_000227685.2:WP_006746339.1 Length = 469 Score = 707 bits (1826), Expect = 0.0 Identities = 336/469 (71%), Positives = 392/469 (83%) Query: 1 MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60 MSA VL + E EVKF+D RFTD+KGKEQHVT+PAH+++ + FE+GKMFDGSSI GWKG Sbjct: 1 MSAADVLKTIQEKEVKFIDFRFTDSKGKEQHVTVPAHEIDEDTFEDGKMFDGSSIAGWKG 60 Query: 61 INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTG 120 INESDM+LMPDA +AV+DPFF D TL +RCD++EP T+QGYDR PRS+ KRAE YL STG Sbjct: 61 INESDMILMPDAGSAVLDPFFEDLTLNLRCDVVEPATMQGYDRCPRSLGKRAEAYLASTG 120 Query: 121 IADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGY 180 IADT LFGPE EFF+ DD+++G+S+SGS+ +D E +WNS YE GN GHRP VKGGY Sbjct: 121 IADTALFGPENEFFVLDDVKWGTSLSGSYCRVDSSEASWNSERVYEDGNIGHRPTVKGGY 180 Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240 FPVPPVDS DIRS MC V+++MGL E HHHEVATAGQ E+ +T+KADE+QI K Sbjct: 181 FPVPPVDSLHDIRSTMCDVLDEMGLHTEVHHHEVATAGQCEIGVGAAMLTRKADEVQILK 240 Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIG 300 YVV NVAH GKTATFMPKP+ GDNGSGMH HMSL+K+G NLF+GD Y GLSE ALYYIG Sbjct: 241 YVVQNVAHAHGKTATFMPKPIVGDNGSGMHVHMSLAKDGTNLFSGDLYGGLSETALYYIG 300 Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVR 360 G+IKHA+A+NA NP+TNSYKRLVPG+EAPVMLAYSARNRSASIRIP V SPKARRIEVR Sbjct: 301 GIIKHARALNAFTNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPFVMSPKARRIEVR 360 Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420 FPD ANPYL FAA+LMAG+DGI+NKIHPG+AMDKNLYDLPPEE K IPQV +L++AL Sbjct: 361 FPDSTANPYLAFAAMLMAGIDGIQNKIHPGDAMDKNLYDLPPEEEKNIPQVCNALDQALR 420 Query: 421 ELDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469 ELD DR FL AGGVFTD+ IDAYI+L+ EE R+RMT HPVEF++YYS+ Sbjct: 421 ELDNDRAFLTAGGVFTDDMIDAYISLKMEEVTRLRMTTHPVEFDMYYSL 469 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: 736 Number of extensions: 19 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_006746339.1 THITH_RS01240 (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.23696.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-207 673.2 0.0 1.1e-206 673.0 0.0 1.0 1 lcl|NCBI__GCF_000227685.2:WP_006746339.1 THITH_RS01240 glutamate--ammonia Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000227685.2:WP_006746339.1 THITH_RS01240 glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 673.0 0.0 1.1e-206 1.1e-206 2 462 .] 5 468 .. 4 468 .. 0.99 Alignments for each domain: == domain 1 score: 673.0 bits; conditional E-value: 1.1e-206 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +vlk+++e++vkf+d+rf+D kGk+++v++p++e++e+++e+g++FDgss+ G+k+i+esD++l+pd+ lcl|NCBI__GCF_000227685.2:WP_006746339.1 5 DVLKTIQEKEVKFIDFRFTDSKGKEQHVTVPAHEIDEDTFEDGKMFDGSSIAGWKGINESDMILMPDAG 73 68899**************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 ++v +Pf ++ +l+++cdv ep+t++ y+r+pRs krae +l t+++d++ fGpE+EFf++d+v+ + lcl|NCBI__GCF_000227685.2:WP_006746339.1 74 SAVLDPFFEDLTLNLRCDVVEPATMQGYDRCPRSLGKRAEAYLAsTGIADTALFGPENEFFVLDDVKWG 142 ********************************************9************************ PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 ++ + s+ +vds e++wn r +e gn g++++ kggYf+v+pvD+++dir+ ++ +l+e+gl++ev+H lcl|NCBI__GCF_000227685.2:WP_006746339.1 143 TSLSGSYCRVDSSEASWNseRVYEDGNIGHRPTVKGGYFPVPPVDSLHDIRSTMCDVLDEMGLHTEVHH 211 ******************99999********************************************** PP TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273 HEvata q Ei++ + l+++aDe++++Kyvv+nva+ hGktatFmpKp++gdngsGmHvh+sl kdg lcl|NCBI__GCF_000227685.2:WP_006746339.1 212 HEVATAgQCEIGVGAAMLTRKADEVQILKYVVQNVAHAHGKTATFMPKPIVGDNGSGMHVHMSLAKDGT 280 ********************************************************************* PP TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342 nlf+g+ y gLsetalyyigGi+kHa+al+A+tnp++nsYkRLvpG+EAPv+laysa+nRsa+iRiP lcl|NCBI__GCF_000227685.2:WP_006746339.1 281 NLFSGDL-YGGLSETALYYIGGIIKHARALNAFTNPSTNSYKRLVPGFEAPVMLAYSARNRSASIRIPF 348 *******.************************************************************* PP TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411 +++pka+RiEvR+pD++anpYLafaa+lmAg+dGi+nki+pg+++dknly+l++ee k+ i+q+ + L lcl|NCBI__GCF_000227685.2:WP_006746339.1 349 VMSPKARRIEVRFPDSTANPYLAFAAMLMAGIDGIQNKIHPGDAMDKNLYDLPPEEEKN--IPQVCNAL 415 *********************************************************99..******** PP TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 ++al el++d+ +++++v+++++i+a+i+lk++Ev +lr++ hpvE+ +y++ lcl|NCBI__GCF_000227685.2:WP_006746339.1 416 DQALRELDNDRafLTAGGVFTDDMIDAYISLKMEEVTRLRMTTHPVEFDMYYS 468 ***********9999************************************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12.21 // [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