Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_019867633.1 METMI_RS0117695 glutamate--ammonia ligase
Query= BRENDA::P0A1P6 (469 letters) >NCBI__GCF_000384075.1:WP_019867633.1 Length = 469 Score = 709 bits (1829), Expect = 0.0 Identities = 335/469 (71%), Positives = 391/469 (83%) Query: 1 MSAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKG 60 MS +HVL ++ E++VKFVD RF DT+GKEQHVT PAH ++ + FEEG MFDGSSI GWK Sbjct: 1 MSVKHVLKLIQENDVKFVDFRFCDTRGKEQHVTFPAHSIDEDTFEEGNMFDGSSIAGWKH 60 Query: 61 INESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATG 120 INESDM+LMPD STAV+DPF+ D+TLIIRCDI+EP +QGY+RDPRS+AKRAE YL++TG Sbjct: 61 INESDMILMPDPSTAVMDPFYDDNTLIIRCDIIEPKNMQGYERDPRSLAKRAEAYLKSTG 120 Query: 121 IADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGY 180 IADT FGPE EFF+FDDIR+G+ +SGS ID E WNS YE GN GHRPG+KGGY Sbjct: 121 IADTAFFGPENEFFIFDDIRWGSDMSGSFFKIDSQEAGWNSEKVYEDGNIGHRPGIKGGY 180 Query: 181 FPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYK 240 FPVPPVDS QDIRS MCL +EQ G++ E HHHEVATAGQ E+ +FNT+ KKADE+ K Sbjct: 181 FPVPPVDSFQDIRSAMCLTLEQFGMMTEVHHHEVATAGQCEIGVKFNTLVKKADEVLGLK 240 Query: 241 YVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIG 300 YVV N+AH +GKTATFMPKPM GDNGSGMH H SLAK+G NLFSGD Y GLSE ALYYIG Sbjct: 241 YVVANIAHAYGKTATFMPKPMVGDNGSGMHVHQSLAKDGVNLFSGDLYGGLSETALYYIG 300 Query: 301 GVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVR 360 G+IKHAKA+NA N +TNSYKRLVPG+EAPVMLAYSARNRSASIRIP V++PK RRIEVR Sbjct: 301 GIIKHAKALNAFTNASTNSYKRLVPGFEAPVMLAYSARNRSASIRIPFVSNPKGRRIEVR 360 Query: 361 FPDPAANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALN 420 FPD ANPYL F+A+LMAGLDGI+NKIHPGEAMDK+LYDLPPEE K IPQV + ++AL+ Sbjct: 361 FPDSTANPYLAFSAMLMAGLDGIQNKIHPGEAMDKDLYDLPPEEEKAIPQVCHAFDQALD 420 Query: 421 ALDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469 ALD DREFL GGVFTD+ ID YI L+ +E R+RM+ HPVEF++YYS+ Sbjct: 421 ALDKDREFLTRGGVFTDDVIDGYIELKMQEVTRLRMSTHPVEFDMYYSL 469 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: 804 Number of extensions: 23 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_019867633.1 METMI_RS0117695 (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.24022.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-210 684.3 0.0 4.3e-210 684.1 0.0 1.0 1 lcl|NCBI__GCF_000384075.1:WP_019867633.1 METMI_RS0117695 glutamate--ammon Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019867633.1 METMI_RS0117695 glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 684.1 0.0 4.3e-210 4.3e-210 2 462 .] 5 468 .. 4 468 .. 0.99 Alignments for each domain: == domain 1 score: 684.1 bits; conditional E-value: 4.3e-210 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +vlkl++e++vkfvd+rf+D++Gk+++v++p+++++e+++eeg +FDgss+ G+k+i+esD++l+pdp+ lcl|NCBI__GCF_000384075.1:WP_019867633.1 5 HVLKLIQENDVKFVDFRFCDTRGKEQHVTFPAHSIDEDTFEEGNMFDGSSIAGWKHINESDMILMPDPS 73 7899***************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 t+v++Pf ++++l+++cd+ ep +++ yerdpRs akrae +lk t+++d+++fGpE+EFf+fd+++ + lcl|NCBI__GCF_000384075.1:WP_019867633.1 74 TAVMDPFYDDNTLIIRCDIIEPKNMQGYERDPRSLAKRAEAYLKsTGIADTAFFGPENEFFIFDDIRWG 142 ********************************************************************* PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 + ++ sf+++ds+e+ wn + +e gn g+++ kggYf+v+pvD+ +dir+ ++l+le++g+ +ev+H lcl|NCBI__GCF_000384075.1:WP_019867633.1 143 SDMSGSFFKIDSQEAGWNseKVYEDGNIGHRPGIKGGYFPVPPVDSFQDIRSAMCLTLEQFGMMTEVHH 211 ******************98889999******************************************* PP TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273 HEvata q Ei++kf++lvk+aDe++ +Kyvv n+a+ +GktatFmpKp++gdngsGmHvh+sl kdg lcl|NCBI__GCF_000384075.1:WP_019867633.1 212 HEVATAgQCEIGVKFNTLVKKADEVLGLKYVVANIAHAYGKTATFMPKPMVGDNGSGMHVHQSLAKDGV 280 ********************************************************************* PP TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342 nlf+g+ y gLsetalyyigGi+kHakal+A+tn+++nsYkRLvpG+EAPv+laysa+nRsa+iRiP lcl|NCBI__GCF_000384075.1:WP_019867633.1 281 NLFSGDL-YGGLSETALYYIGGIIKHAKALNAFTNASTNSYKRLVPGFEAPVMLAYSARNRSASIRIPF 348 *******.************************************************************* PP TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411 ++npk++RiEvR+pD++anpYLaf+a+lmAgldGi+nki+pge++dk+ly+l++ee k i+q+ + lcl|NCBI__GCF_000384075.1:WP_019867633.1 349 VSNPKGRRIEVRFPDSTANPYLAFSAMLMAGLDGIQNKIHPGEAMDKDLYDLPPEEEKA--IPQVCHAF 415 ********************************************************999..******** PP TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 ++ald+l++d+ ++ ++v+++++i+ +ielk++Ev +lr++ hpvE+ +y++ lcl|NCBI__GCF_000384075.1:WP_019867633.1 416 DQALDALDKDRefLTRGGVFTDDVIDGYIELKMQEVTRLRMSTHPVEFDMYYS 468 ***********888999**********************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.54 // [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