Align glutamate--ammonia ligase; EC 6.3.1.2 (characterized)
to candidate WP_029935560.1 N746_RS0107975 type I glutamate--ammonia ligase
Query= CharProtDB::CH_024014 (469 letters) >NCBI__GCF_000711195.1:WP_029935560.1 Length = 468 Score = 644 bits (1661), Expect = 0.0 Identities = 306/464 (65%), Positives = 369/464 (79%) Query: 6 VLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGINESD 65 ++ ++ E +VK+ DLRFTD+ GKEQHVTIPAH+V+ EFFE+G FDGSSI GWKGI SD Sbjct: 5 IIDLIKEQDVKWADLRFTDSIGKEQHVTIPAHEVDDEFFEDGHNFDGSSIRGWKGIQSSD 64 Query: 66 MVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRSTGIADTV 125 MVLMP +DPF D T+IIRC I+EP TL+ Y++DPR I+K+AE YL+STGIADT Sbjct: 65 MVLMPQTDGFYLDPFTNDPTIIIRCMIVEPSTLEPYEKDPRGISKKAEVYLQSTGIADTA 124 Query: 126 LFGPEPEFFLFDDIRFGSSISGSHVAIDDIEGAWNSSTQYEGGNKGHRPAVKGGYFPVPP 185 FGPEPEFF+FDD+R+G+ +SGS V ID E AWN+ Y GN GHRP VKGGYFPVPP Sbjct: 125 FFGPEPEFFIFDDVRWGADMSGSFVKIDGNEAAWNTEKVYTDGNMGHRPRVKGGYFPVPP 184 Query: 186 VDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKYVVHN 245 VD ++R+++C + E MGL +EAHHHEVA AGQ E+A NT+TKKADE+QI KY VHN Sbjct: 185 VDQLHEVRADICAMAEAMGLKIEAHHHEVAAAGQCELAVAGNTLTKKADEVQILKYAVHN 244 Query: 246 VAHRFGKTATFMPKPMFGDNGSGMHCHMSLSKNGVNLFAGDKYAGLSEQALYYIGGVIKH 305 H GKTATFMPKP+ GDNGSGMH +MSL+K G N+FAGD Y+GLS++AL+YIGG++KH Sbjct: 245 TCHAVGKTATFMPKPIVGDNGSGMHINMSLNKGGKNIFAGDVYSGLSQEALWYIGGLMKH 304 Query: 306 AKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVSSPKARRIEVRFPDPA 365 A+A+NA NP TNSYKRLVPG+EAP++LAYS NRSASIRIP S +ARR+E+RFPDP Sbjct: 305 ARALNAFTNPGTNSYKRLVPGFEAPILLAYSGSNRSASIRIPYAPSERARRVELRFPDPT 364 Query: 366 ANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNELDLD 425 ANPYL FAA LMAGLDGI NKI PGE +K+LYDLPPEE V SLEEAL+ LD D Sbjct: 365 ANPYLAFAASLMAGLDGIINKIDPGEPAEKDLYDLPPEEEATYNTVCASLEEALDALDKD 424 Query: 426 REFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469 REFLKAGGVFTDEAID+YI L+ EE R+R T HP+EF++YYS+ Sbjct: 425 REFLKAGGVFTDEAIDSYIKLKMEEVTRMRATTHPIEFDMYYSM 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: 768 Number of extensions: 30 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: 468 Length adjustment: 33 Effective length of query: 436 Effective length of database: 435 Effective search space: 189660 Effective search space used: 189660 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_029935560.1 N746_RS0107975 (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.2728.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-192 626.9 0.0 1.1e-192 626.7 0.0 1.0 1 lcl|NCBI__GCF_000711195.1:WP_029935560.1 N746_RS0107975 type I glutamate- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711195.1:WP_029935560.1 N746_RS0107975 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 626.7 0.0 1.1e-192 1.1e-192 2 462 .] 4 467 .. 3 467 .. 0.99 Alignments for each domain: == domain 1 score: 626.7 bits; conditional E-value: 1.1e-192 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 ++++l+ke++vk dlrf+D Gk+++v+ip++e+++e++e+g FDgss++G+k+i+ sD++l+p+++ lcl|NCBI__GCF_000711195.1:WP_029935560.1 4 TIIDLIKEQDVKWADLRFTDSIGKEQHVTIPAHEVDDEFFEDGHNFDGSSIRGWKGIQSSDMVLMPQTD 72 68999**************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 + +Pf+++++++++c + ep t epye+dpR i k+ae +l+ t+++d+++fGpE+EFf+fd+v+ + lcl|NCBI__GCF_000711195.1:WP_029935560.1 73 GFYLDPFTNDPTIIIRCMIVEPSTLEPYEKDPRGISKKAEVYLQsTGIADTAFFGPEPEFFIFDDVRWG 141 ********************************************************************* PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 ++ sf+++d +e++wn + + gn g++++ kggYf+v+pvD+++++r +++ + e++gl++e++H lcl|NCBI__GCF_000711195.1:WP_029935560.1 142 ADMSGSFVKIDGNEAAWNteKVYTDGNMGHRPRVKGGYFPVPPVDQLHEVRADICAMAEAMGLKIEAHH 210 ******************87778888******************************************* PP TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273 HEva a q E+++ ++l+k+aDe++++Ky+v+n+ + GktatFmpKp++gdngsGmH+++sl k g+ lcl|NCBI__GCF_000711195.1:WP_029935560.1 211 HEVAAAgQCELAVAGNTLTKKADEVQILKYAVHNTCHAVGKTATFMPKPIVGDNGSGMHINMSLNKGGK 279 *****99************************************************************** PP TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342 n+fag+ y+gLs++al+yigG++kHa+al+A+tnp +nsYkRLvpG+EAP+ lays +nRsa+iRiP+ lcl|NCBI__GCF_000711195.1:WP_029935560.1 280 NIFAGDV-YSGLSQEALWYIGGLMKHARALNAFTNPGTNSYKRLVPGFEAPILLAYSGSNRSASIRIPY 347 *******.************************************************************* PP TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411 + +++a+R+E+R+pDp+anpYLafaa lmAgldGi nkidpgep +k+ly+l++ee + +++ +sL lcl|NCBI__GCF_000711195.1:WP_029935560.1 348 APSERARRVELRFPDPTANPYLAFAASLMAGLDGIINKIDPGEPAEKDLYDLPPEEEAT--YNTVCASL 414 ********************************************************999..9******* PP TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 eeald+l++d+ +++++v+++e+i+++i+lk++Ev ++r + hp+E+ +y++ lcl|NCBI__GCF_000711195.1:WP_029935560.1 415 EEALDALDKDRefLKAGGVFTDEAIDSYIKLKMEEVTRMRATTHPIEFDMYYS 467 ***********888899**********************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (468 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: 7.69 // [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