Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate WP_013418231.1 RVAN_RS02710 type I glutamate--ammonia ligase
Query= CharProtDB::CH_024014 (469 letters) >NCBI__GCF_000166055.1:WP_013418231.1 Length = 469 Score = 632 bits (1630), Expect = 0.0 Identities = 306/467 (65%), Positives = 360/467 (77%), Gaps = 1/467 (0%) Query: 2 SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGI 61 +A V+ L + +++FVDLRFTD +GK QHVT+ ++ + F EG MFDGSSI GWK I Sbjct: 3 NASEVVKKLKDEDIRFVDLRFTDPRGKLQHVTMETSEMGEDAFAEGIMFDGSSIAGWKAI 62 Query: 62 NESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTGI 121 NESDM LMPD TA +DPFFA STL I CDILEP T + Y+RDPR IA++AE YL+ TGI Sbjct: 63 NESDMTLMPDPETAHLDPFFAQSTLAIFCDILEPATGERYERDPRGIARKAEAYLKQTGI 122 Query: 122 ADTVLFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGYF 181 DT FGPE EFF+FDD+RF + +D E N T+YE GN GHRP KGGYF Sbjct: 123 GDTAYFGPEAEFFIFDDVRFSADPYNCGYRLDSSELPSNMGTEYEMGNLGHRPRTKGGYF 182 Query: 182 PVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKY 241 PVPPVDSAQDIRSEM M MG+ E HHHEVA A Q+E+ +F T+T AD +QIYKY Sbjct: 183 PVPPVDSAQDIRSEMLSTMAAMGVKTEKHHHEVAAA-QHELGIKFGTLTTTADAMQIYKY 241 Query: 242 VVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIGG 301 V HNVA +GKTATFMPKP+FGDNGSGMH H S+ K +FAG +YA LSE L+YIGG Sbjct: 242 VTHNVAQSYGKTATFMPKPVFGDNGSGMHVHQSIWKGSEPVFAGSEYADLSETCLFYIGG 301 Query: 302 VIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVRF 361 ++KHAKA+NA NP+TNSYKRLVPGYEAPV+ AYS+RNRSAS RIPVVSSPK +R+EVRF Sbjct: 302 ILKHAKALNAFTNPSTNSYKRLVPGYEAPVLRAYSSRNRSASCRIPVVSSPKGKRVEVRF 361 Query: 362 PDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNE 421 PDP ANPYL F+A+LMAGLDGIKN+IHPG+ MDKNLYDLP E +EIP V GSL+EA++ Sbjct: 362 PDPTANPYLAFSAMLMAGLDGIKNRIHPGQPMDKNLYDLPEAELREIPTVCGSLQEAIDS 421 Query: 422 LDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYS 468 LD DR FLK GGVFTD+ IDAYIAL+ EE DR RM PHP+EFE+YYS Sbjct: 422 LDADRTFLKEGGVFTDDQIDAYIALKVEEIDRFRMMPHPIEFEMYYS 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: 763 Number of extensions: 26 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_013418231.1 RVAN_RS02710 (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.10196.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-207 675.1 0.0 2.8e-207 674.9 0.0 1.0 1 lcl|NCBI__GCF_000166055.1:WP_013418231.1 RVAN_RS02710 type I glutamate--a Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000166055.1:WP_013418231.1 RVAN_RS02710 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 674.9 0.0 2.8e-207 2.8e-207 2 462 .] 6 468 .. 5 468 .. 0.99 Alignments for each domain: == domain 1 score: 674.9 bits; conditional E-value: 2.8e-207 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 ev+k lk+e+++fvdlrf+D +Gkl++v++ se+ e+a+ egi+FDgss+ G+k+i+esD+ l+pdpe lcl|NCBI__GCF_000166055.1:WP_013418231.1 6 EVVKKLKDEDIRFVDLRFTDPRGKLQHVTMETSEMGEDAFAEGIMFDGSSIAGWKAINESDMTLMPDPE 74 688999*************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 t+ +Pf a+++l ++cd+ ep+t+e+yerdpR ia++ae +lk t++gd++yfGpEaEFf+fd+v+f+ lcl|NCBI__GCF_000166055.1:WP_013418231.1 75 TAHLDPFFAQSTLAIFCDILEPATGERYERDPRGIARKAEAYLKqTGIGDTAYFGPEAEFFIFDDVRFS 143 ********************************************************************* PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 + +++ds e n +e+e gn g+++++kggYf+v+pvD+a+dir+e++++++++g+++e++H lcl|NCBI__GCF_000166055.1:WP_013418231.1 144 ADPYNCGYRLDSSELPSNmgTEYEMGNLGHRPRTKGGYFPVPPVDSAQDIRSEMLSTMAAMGVKTEKHH 212 *************98877779************************************************ PP TIGR00653 206 HEvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274 HEva aq+E++ikf +l+++aD++++yKyv +nva+ +GktatFmpKp+fgdngsGmHvh+s+wk e+ lcl|NCBI__GCF_000166055.1:WP_013418231.1 213 HEVAAAQHELGIKFGTLTTTADAMQIYKYVTHNVAQSYGKTATFMPKPVFGDNGSGMHVHQSIWKGSEP 281 ********************************************************************* PP TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343 +fag+e ya+Lset+l+yigGilkHakal+A+tnp++nsYkRLvpGyEAPv ays +nRsa+ RiP++ lcl|NCBI__GCF_000166055.1:WP_013418231.1 282 VFAGSE-YADLSETCLFYIGGILKHAKALNAFTNPSTNSYKRLVPGYEAPVLRAYSSRNRSASCRIPVV 349 ******.************************************************************** PP TIGR00653 344 anpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLe 412 ++pk+kR+EvR+pDp+anpYLaf+a+lmAgldGikn+i+pg+p+dknly+l+e+el+e i+++ sL+ lcl|NCBI__GCF_000166055.1:WP_013418231.1 350 SSPKGKRVEVRFPDPTANPYLAFSAMLMAGLDGIKNRIHPGQPMDKNLYDLPEAELRE--IPTVCGSLQ 416 **********************************************************..********* PP TIGR00653 413 ealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 ea+d+l++d+ +++++v++++ i+a+i+lk +E++++r+ +hp+E+e+y++ lcl|NCBI__GCF_000166055.1:WP_013418231.1 417 EAIDSLDADRtfLKEGGVFTDDQIDAYIALKVEEIDRFRMMPHPIEFEMYYS 468 **********999999**********************************96 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 10.46 // [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