Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate WP_012589471.1 MSIL_RS02165 type I glutamate--ammonia ligase
Query= CharProtDB::CH_024014 (469 letters) >NCBI__GCF_000021745.1:WP_012589471.1 Length = 469 Score = 608 bits (1567), Expect = e-178 Identities = 295/463 (63%), Positives = 354/463 (76%), Gaps = 1/463 (0%) Query: 6 VLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGINESD 65 VL + +++VK+VD RFTD +GK QHVT ++ + F EG MFDGSSI GWK INESD Sbjct: 7 VLKEIKDNDVKYVDFRFTDPRGKWQHVTFDISLIDEDIFAEGTMFDGSSIAGWKAINESD 66 Query: 66 MVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTGIADTV 125 M+LMPD STAV+DPFFA T++I CDILEP + + Y RDPR IAK+AE +L S+GI D+V Sbjct: 67 MLLMPDPSTAVMDPFFAAPTMVIVCDILEPNSNEPYSRDPRGIAKKAEAFLVSSGIGDSV 126 Query: 126 LFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGYFPVPP 185 GPE EFF+FDD+R+ + + +D E NS T YEGGN GHR KGGYFPVPP Sbjct: 127 FVGPEAEFFVFDDVRYRADPYNTGFVLDSAELPSNSDTPYEGGNLGHRIRTKGGYFPVPP 186 Query: 186 VDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKYVVHN 245 DSAQD+R EM M MG VE HHHEVA+A Q+E+ +F +T AD +Q+YKY +H Sbjct: 187 QDSAQDMRGEMLAAMAAMGAKVEKHHHEVASA-QHELGLKFGPLTTMADHLQVYKYCIHQ 245 Query: 246 VAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIGGVIKH 305 VA +GKTATFMPKP+FGDNGSGMH H S+ K G LFAGDKYA LS++ LYYIGG+I+H Sbjct: 246 VAQSYGKTATFMPKPVFGDNGSGMHVHQSIWKGGKPLFAGDKYADLSQECLYYIGGIIRH 305 Query: 306 AKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVRFPDPA 365 A+A+NA NP+TNSYKRLVPGYEAPV+LAYSARNRSAS RIP S+PKA+R+EVRFPDP Sbjct: 306 ARALNAFTNPSTNSYKRLVPGYEAPVLLAYSARNRSASCRIPTASNPKAKRVEVRFPDPM 365 Query: 366 ANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNELDLD 425 ANPYL F+A+LMAGLDGI NKI PG AMDK+LYDLPP E K+IP V GSL EAL LD D Sbjct: 366 ANPYLAFSAMLMAGLDGIINKIDPGPAMDKDLYDLPPRELKKIPTVCGSLREALANLDKD 425 Query: 426 REFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYS 468 R FLKAGGV+ D+ ID+YI L+ + R MTPHPVEF++YYS Sbjct: 426 RAFLKAGGVYDDDFIDSYIELKMADVMRFEMTPHPVEFDMYYS 468 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: 751 Number of extensions: 29 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 WP_012589471.1 MSIL_RS02165 (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.5499.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-198 645.8 0.0 2.1e-198 645.6 0.0 1.0 1 lcl|NCBI__GCF_000021745.1:WP_012589471.1 MSIL_RS02165 type I glutamate--a Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021745.1:WP_012589471.1 MSIL_RS02165 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 645.6 0.0 2.1e-198 2.1e-198 2 462 .] 6 468 .. 5 468 .. 0.99 Alignments for each domain: == domain 1 score: 645.6 bits; conditional E-value: 2.1e-198 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +vlk +k+++vk+vd+rf+D +Gk+++v++ +s ++e+++ eg++FDgss+ G+k+i+esD+ll+pdp+ lcl|NCBI__GCF_000021745.1:WP_012589471.1 6 DVLKEIKDNDVKYVDFRFTDPRGKWQHVTFDISLIDEDIFAEGTMFDGSSIAGWKAINESDMLLMPDPS 74 578999*************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 t+v++Pf a+++++++cd+ ep +epy+rdpR iak+ae l +++gd+v++GpEaEFf+fd+v+ + lcl|NCBI__GCF_000021745.1:WP_012589471.1 75 TAVMDPFFAAPTMVIVCDILEPNSNEPYSRDPRGIAKKAEAFLVsSGIGDSVFVGPEAEFFVFDDVRYR 143 *******************************************999*********************** PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 ++ + +ds e n + +e+gn g++i++kggYf+v+p+D+a+d+r e++ a++++g +ve++H lcl|NCBI__GCF_000021745.1:WP_012589471.1 144 ADPYNTGFVLDSAELPSNsdTPYEGGNLGHRIRTKGGYFPVPPQDSAQDMRGEMLAAMAAMGAKVEKHH 212 9999999*****99888866888999******************************************* PP TIGR00653 206 HEvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274 HEva+aq+E+++kf l+++aD++++yKy +++va+ +GktatFmpKp+fgdngsGmHvh+s+wk g++ lcl|NCBI__GCF_000021745.1:WP_012589471.1 213 HEVASAQHELGLKFGPLTTMADHLQVYKYCIHQVAQSYGKTATFMPKPVFGDNGSGMHVHQSIWKGGKP 281 ********************************************************************* PP TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343 lfag++ ya+Ls+++lyyigGi++Ha+al+A+tnp++nsYkRLvpGyEAPv laysa+nRsa+ RiP++ lcl|NCBI__GCF_000021745.1:WP_012589471.1 282 LFAGDK-YADLSQECLYYIGGIIRHARALNAFTNPSTNSYKRLVPGYEAPVLLAYSARNRSASCRIPTA 349 ******.************************************************************** PP TIGR00653 344 anpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLe 412 +npkakR+EvR+pDp anpYLaf+a+lmAgldGi nkidpg ++dk+ly+l++ elk+ i+++ sL+ lcl|NCBI__GCF_000021745.1:WP_012589471.1 350 SNPKAKRVEVRFPDPMANPYLAFSAMLMAGLDGIINKIDPGPAMDKDLYDLPPRELKK--IPTVCGSLR 416 **********************************************************..********* PP TIGR00653 413 ealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 eal +l++d+ +++++v+ +++i+++ielk+++v ++++++hpvE+ +y++ lcl|NCBI__GCF_000021745.1:WP_012589471.1 417 EALANLDKDRafLKAGGVYDDDFIDSYIELKMADVMRFEMTPHPVEFDMYYS 468 **********999999**********************************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: 00:00:00.02 # Mc/sec: 10.26 // [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