Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I beta; GSI beta; EC 6.3.1.2 (characterized)
to candidate WP_004314445.1 C665_RS13385 type I glutamate--ammonia ligase
Query= SwissProt::Q3V5W6 (468 letters) >NCBI__GCF_000310185.1:WP_004314445.1 Length = 469 Score = 658 bits (1697), Expect = 0.0 Identities = 315/463 (68%), Positives = 376/463 (81%), Gaps = 1/463 (0%) Query: 5 VQLIKDHDVKWIDLRFTDTKGTQHHVTMPARDALEDDFFEVGKMFDGSSIAGWKGIEASD 64 +++I++++V+++DLRFTD +G +HHV +P A E++ FE G FDGSS+AGWKGI+ASD Sbjct: 7 MKMIQENEVRFVDLRFTDIRGKEHHVGLPV-SAFEEEHFEHGHPFDGSSLAGWKGIQASD 65 Query: 65 MILLPDDDTAVLDPFTEDATLILVCDIIEPSTMQGYDRDPRAIAHRAEEYLKTTGIGDTV 124 MIL+P+ TA +DPF ++ TL++ CD+IEPS +GYDRDPR+IA RAE YLK+TGIGDT Sbjct: 66 MILMPEPSTAYIDPFFDETTLVITCDVIEPSDGKGYDRDPRSIAKRAEAYLKSTGIGDTA 125 Query: 125 FAGPEPEFFIFDEVKFKSDISGSMFKIYSEQGSWMSDQDIEGGNKGHRPGVKGGYFPVPP 184 F GPEPEFFIFD V++ D+SG KI SE+ +W + EGGN GHRP VKGGYFPVPP Sbjct: 126 FFGPEPEFFIFDSVEWSVDMSGVYSKIISEEAAWSTADKFEGGNTGHRPRVKGGYFPVPP 185 Query: 185 FDHDHEIRTAMCNALEEMGQTVEVHHHEVATAGQNEIGVKFNTLVKKADEVQTLKYVVHN 244 D +++R AM ALE G VEVHHHEVA AGQ EIG KF+TL ++AD Q LKY+VHN Sbjct: 186 VDSLNDVRAAMVLALEACGVPVEVHHHEVANAGQCEIGTKFSTLTQRADWTQVLKYIVHN 245 Query: 245 VADAYGRTATFMPKPLYGDNGSGMHVHMSIAKDGKNTFAGEGYAGLSETALYFIGGIIKH 304 VA YG+TATFMPKP+ GDNGSGMHVH SI KDGKN FAG GYAGLSETALY+IGGIIKH Sbjct: 246 VAHQYGKTATFMPKPIVGDNGSGMHVHQSIWKDGKNLFAGNGYAGLSETALYYIGGIIKH 305 Query: 305 GKALNGFTNPATNSYKRLVPGFEAPVMLAYSARNRSASIRIPYVNSPRGRRIEARFPDPA 364 +ALN TNP TNSYKRLVP +EAP LAYSARNRSASIRIPYV +P+GRRIE+RFPDP Sbjct: 306 ARALNAITNPGTNSYKRLVPHYEAPTKLAYSARNRSASIRIPYVANPKGRRIESRFPDPL 365 Query: 365 ANPYLAFAALLMAGLDGIQNKIHPGDAADKNLYDLPPEEAKEIPQVCGSLKEALEELDKG 424 ANPY+ FAAL+MAGLDGIQNKIHPGD ADKNLYDLPPEE IP VC SL++ALE LDK Sbjct: 366 ANPYMCFAALMMAGLDGIQNKIHPGDPADKNLYDLPPEEDALIPTVCTSLEQALEYLDKD 425 Query: 425 RAFLTKGGVFSDDFIDAYIALKSEEEIKVRTFVHPLEYELYYS 467 R FLT+GGVFS+DFIDAYIALK EE ++R HP+E+++YYS Sbjct: 426 REFLTRGGVFSNDFIDAYIALKMEEVDRMRITTHPVEFDMYYS 468 Lambda K H 0.318 0.137 0.409 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: 796 Number of extensions: 28 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: 468 Length of database: 469 Length adjustment: 33 Effective length of query: 435 Effective length of database: 436 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_004314445.1 C665_RS13385 (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.26985.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-204 663.9 0.0 6.7e-204 663.7 0.0 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004314445.1 C665_RS13385 type I glutamate--a Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004314445.1 C665_RS13385 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 663.7 0.0 6.7e-204 6.7e-204 2 462 .] 5 468 .. 4 468 .. 0.99 Alignments for each domain: == domain 1 score: 663.7 bits; conditional E-value: 6.7e-204 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +v+k+++e++v+fvdlrf+Di+Gk+++v +pvs++eee +e+g FDgss+ G+k+i+ sD++l+p+p+ lcl|NCBI__GCF_000310185.1:WP_004314445.1 5 DVMKMIQENEVRFVDLRFTDIRGKEHHVGLPVSAFEEEHFEHGHPFDGSSLAGWKGIQASDMILMPEPS 73 789****************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 t+ i+Pf +e++l+++cdv ep +++ y+rdpRsiakrae +lk t++gd+++fGpE+EFf+fd+ve + lcl|NCBI__GCF_000310185.1:WP_004314445.1 74 TAYIDPFFDETTLVITCDVIEPSDGKGYDRDPRSIAKRAEAYLKsTGIGDTAFFGPEPEFFIFDSVEWS 142 ********************************************************************* PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 ++ + ++ see++w+ ++e+gn+g++++ kggYf+v+pvD+++d+r +vlale+ g+ vev+H lcl|NCBI__GCF_000310185.1:WP_004314445.1 143 VDMSGVYSKIISEEAAWStaDKFEGGNTGHRPRVKGGYFPVPPVDSLNDVRAAMVLALEACGVPVEVHH 211 ******************888999********************************************* PP TIGR00653 206 HEvata.qaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdge 273 HEva+a q Ei++kf++l++ aD ++++Ky+v+nva+++GktatFmpKp++gdngsGmHvh+s+wkdg+ lcl|NCBI__GCF_000310185.1:WP_004314445.1 212 HEVANAgQCEIGTKFSTLTQRADWTQVLKYIVHNVAHQYGKTATFMPKPIVGDNGSGMHVHQSIWKDGK 280 ********************************************************************* PP TIGR00653 274 nlfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPa 342 nlfag+ yagLsetalyyigGi+kHa+al+A+tnp +nsYkRLvp yEAP +laysa+nRsa+iRiP+ lcl|NCBI__GCF_000310185.1:WP_004314445.1 281 NLFAGNG-YAGLSETALYYIGGIIKHARALNAITNPGTNSYKRLVPHYEAPTKLAYSARNRSASIRIPY 348 ******9.************************************************************* PP TIGR00653 343 sanpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesL 411 +anpk++RiE R+pDp anpY++faal+mAgldGi+nki+pg+p dknly+l++ee + i+++ +sL lcl|NCBI__GCF_000310185.1:WP_004314445.1 349 VANPKGRRIESRFPDPLANPYMCFAALMMAGLDGIQNKIHPGDPADKNLYDLPPEEDAL--IPTVCTSL 415 ********************************************************999..******** PP TIGR00653 412 eealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 e+al+ l++d+ ++ ++v+++++i+a+i+lk++Ev+++r++ hpvE+ +y++ lcl|NCBI__GCF_000310185.1:WP_004314445.1 416 EQALEYLDKDRefLTRGGVFSNDFIDAYIALKMEEVDRMRITTHPVEFDMYYS 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: 7.76 // [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