Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_011383139.1 AMB_RS03575 type I glutamate--ammonia ligase
Query= BRENDA::P0A1P6 (469 letters) >NCBI__GCF_000009985.1:WP_011383139.1 Length = 470 Score = 596 bits (1537), Expect = e-175 Identities = 290/464 (62%), Positives = 354/464 (76%), Gaps = 1/464 (0%) Query: 6 VLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGINESD 65 VL ++ E++VK+VD RFTD +GK QH V+A+ EG MFDGSSI GWK INESD Sbjct: 8 VLELIKENDVKYVDFRFTDPRGKWQHTAQHVSTVDADMLNEGIMFDGSSIAGWKSINESD 67 Query: 66 MVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATGIADTV 125 M+L PDAS+AV+DPF A S LII CDI+EP T Q YDRDPRSIAKRAE Y++++G+ D Sbjct: 68 MILKPDASSAVMDPFAAQSQLIINCDIVEPATGQLYDRDPRSIAKRAEAYVKSSGVGDAT 127 Query: 126 LFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGYFPVPP 185 FGPE EFF+FDD+++ ++ + + +G + GN GHRPGVKGGYFPVPP Sbjct: 128 YFGPEAEFFVFDDVKYELGMNKGYYELRSEDGVEAQGRDFAEGNLGHRPGVKGGYFPVPP 187 Query: 186 VDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKYVVHN 245 VD D+R+EM VM +MGL +E HHHEVA++ Q+E+ +F ++ + AD IQIYKYVVHN Sbjct: 188 VDGHVDMRAEMLTVMGEMGLPIEKHHHEVASS-QHELGIKFGSLVEAADWIQIYKYVVHN 246 Query: 246 VAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIGGVIKH 305 VA +GKTATFMPKP++GDNGSGMH H S+ K G LF+G YA LS+ ALYYIGG+IKH Sbjct: 247 VAASYGKTATFMPKPIYGDNGSGMHVHQSIWKAGKPLFAGSGYADLSDTALYYIGGIIKH 306 Query: 306 AKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVRFPDPA 365 AKAINA NP TNSYKRL+PG+EAPV+LAYSARNRSAS RIP ASPK +R+EVRFPDP Sbjct: 307 AKAINAFTNPLTNSYKRLIPGFEAPVLLAYSARNRSASCRIPYSASPKGKRVEVRFPDPG 366 Query: 366 ANPYLCFAALLMAGLDGIKNKIHPGEAMDKNLYDLPPEEAKEIPQVAGSLEEALNALDLD 425 ANPYL F+A+LMAGLDGI NKIHPG+ MDKNLYDLPPEE K++P V GSL EAL AL + Sbjct: 367 ANPYLAFSAMLMAGLDGIANKIHPGDPMDKNLYDLPPEELKQVPTVCGSLREALEALRAN 426 Query: 426 REFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV 469 +FL G VF+ E I++YI L+ EE R TPHPVEF++YYSV Sbjct: 427 SDFLCKGDVFSKEFIESYIELKYEEVYRFEHTPHPVEFQMYYSV 470 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: 750 Number of extensions: 33 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: 470 Length adjustment: 33 Effective length of query: 436 Effective length of database: 437 Effective search space: 190532 Effective search space used: 190532 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_011383139.1 AMB_RS03575 (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.16543.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-203 660.5 0.0 7.1e-203 660.4 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011383139.1 AMB_RS03575 type I glutamate--am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011383139.1 AMB_RS03575 type I glutamate--ammonia ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 660.4 0.0 7.1e-203 7.1e-203 2 462 .] 7 469 .. 6 469 .. 0.99 Alignments for each domain: == domain 1 score: 660.4 bits; conditional E-value: 7.1e-203 TIGR00653 2 evlkllkeenvkfvdlrfvDikGklkkveipvseleeealeegiaFDgssveGfksieesDlllkpdpe 70 +vl+l+ke++vk+vd+rf+D +Gk+++ + vs++++++l+egi+FDgss+ G+ksi+esD++lkpd++ lcl|NCBI__GCF_000009985.1:WP_011383139.1 7 KVLELIKENDVKYVDFRFTDPRGKWQHTAQHVSTVDADMLNEGIMFDGSSIAGWKSINESDMILKPDAS 75 7899***************************************************************** PP TIGR00653 71 tlvivPfraekvlrvicdvyepvtkepyerdpRsiakraeeelk.tklgdevyfGpEaEFflfdkvefk 138 ++v++Pf+a++ l+++cd+ ep+t++ y+rdpRsiakrae ++k +++gd +yfGpEaEFf+fd+v+ + lcl|NCBI__GCF_000009985.1:WP_011383139.1 76 SAVMDPFAAQSQLIINCDIVEPATGQLYDRDPRSIAKRAEAYVKsSGVGDATYFGPEAEFFVFDDVKYE 144 ********************************************99*********************** PP TIGR00653 139 easnssflevdseegewn..reveegnkgykikkkggYfdvepvDkakdirrelvlaleelglevevsH 205 +n+ ++e+ se+g r++ egn g+++ kggYf+v+pvD +d+r e+++++ e+gl +e++H lcl|NCBI__GCF_000009985.1:WP_011383139.1 145 LGMNKGYYELRSEDGVEAqgRDFAEGNLGHRPGVKGGYFPVPPVDGHVDMRAEMLTVMGEMGLPIEKHH 213 **************986557************************************************* PP TIGR00653 206 HEvataqaEidikfdklvkaaDeivlyKyvvknvakkhGktatFmpKplfgdngsGmHvhlslwkdgen 274 HEva++q+E++ikf +lv+aaD i++yKyvv+nva+ +GktatFmpKp++gdngsGmHvh+s+wk g++ lcl|NCBI__GCF_000009985.1:WP_011383139.1 214 HEVASSQHELGIKFGSLVEAADWIQIYKYVVHNVAASYGKTATFMPKPIYGDNGSGMHVHQSIWKAGKP 282 ********************************************************************* PP TIGR00653 275 lfageegyagLsetalyyigGilkHakalaAltnptvnsYkRLvpGyEAPvylaysaknRsaliRiPas 343 lfag+ ya+Ls+talyyigGi+kHaka++A+tnp +nsYkRL+pG+EAPv laysa+nRsa+ RiP+s lcl|NCBI__GCF_000009985.1:WP_011383139.1 283 LFAGSG-YADLSDTALYYIGGIIKHAKAINAFTNPLTNSYKRLIPGFEAPVLLAYSARNRSASCRIPYS 350 *****9.************************************************************** PP TIGR00653 344 anpkakRiEvRspDpsanpYLafaallmAgldGiknkidpgepldknlyelseeelkelGieqlpesLe 412 a+pk+kR+EvR+pDp anpYLaf+a+lmAgldGi nki+pg+p+dknly+l++eelk+ ++++ sL+ lcl|NCBI__GCF_000009985.1:WP_011383139.1 351 ASPKGKRVEVRFPDPGANPYLAFSAMLMAGLDGIANKIHPGDPMDKNLYDLPPEELKQ--VPTVCGSLR 417 **********************************************************..********* PP TIGR00653 413 ealdelesdk..evlkevlgeelieafielkrkEveelrlkvhpvElekyld 462 eal++l +++ + +++v+++e+ie++ielk +Ev +++ ++hpvE+++y++ lcl|NCBI__GCF_000009985.1:WP_011383139.1 418 EALEALRANSdfLCKGDVFSKEFIESYIELKYEEVYRFEHTPHPVEFQMYYS 469 ******998877999***********************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (462 nodes) Target sequences: 1 (470 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: 7.69 // [ok]
This GapMind analysis is from Apr 09 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