Alignments for a candidate for gatE in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatE in Methanococcus maripaludis C5

Align glutamyl-tRNA(Gln) amidotransferase subunit E (EC 6.3.5.7) (characterized)
to candidate WP_011868096.1 MMARC5_RS01665 Glu-tRNA(Gln) amidotransferase subunit GatE

Query= metacyc::MONOMER-14999
         (619 letters)



>NCBI__GCF_000016125.1:WP_011868096.1
          Length = 631

 Score =  616 bits (1588), Expect = e-180
 Identities = 319/633 (50%), Positives = 457/633 (72%), Gaps = 21/633 (3%)

Query: 2   DWEKVGLKMGLEIHQQLDTESKLFCPCRTELTDSEPDHDIVRNLRPTQSELGKFDRAAFE 61
           D+EK+GLK+GLEIHQQL+T+ KLFC C T++ D EP  +I R LRP+QSE+G  D+AA  
Sbjct: 4   DYEKLGLKVGLEIHQQLNTKRKLFCNCPTKIRDDEPHGEIERVLRPSQSEMGHVDKAALL 63

Query: 62  EAMRKLHFHYENYHEETCLVEADEEPPHPLNPEALEIAVTIALLLNMRVVDEFHTMRKQV 121
           E+ ++  F Y+ Y++ TCLVE D+EPPH ++PEA++ A+ ++ L+NM++ DE   MRK V
Sbjct: 64  ESKKEKKFIYQYYNDSTCLVELDDEPPHDVSPEAVDTALEVSTLMNMKMADEVQIMRKMV 123

Query: 122 IDGSNTGGFQRTGLVATDGHLETPQGTVKIENLCLEEDAARRIRETGDGVVFRLDRLGIP 181
           IDGSNT GFQRT  V+ +G +ET  G + + +LCLEEDA ++I +  D   + +DRLGIP
Sbjct: 124 IDGSNTSGFQRTMFVSQEGFIETEYGNIGVTSLCLEEDACKKIEDGKDYTKYCVDRLGIP 183

Query: 182 LVEITTDPSMSDPQQLREVAYQIGQILRST-RVKRGLGTIRQDLNISIRDGARVEVKGVQ 240
           L+EITT+P ++ P+  +E A +IG ILR+T +VKRGLGTIRQD+NISIR+GAR+EVKGVQ
Sbjct: 184 LLEITTEPDITSPKMGKEAARRIGTILRATGKVKRGLGTIRQDVNISIREGARIEVKGVQ 243

Query: 241 DLDLIPEIVEREVKRQLSLVEIRDTLQERGAVVEDKIFDVSEVFADTESRIISSAES--- 297
           +LDLI +I+E EV RQ+SL EI++ L +R A V D+I D++E+  DTES+++ SA     
Sbjct: 244 NLDLIEKIIENEVTRQISLNEIKEELLKRNAEVVDEIKDITELLKDTESKVLKSALKNKG 303

Query: 298 -VLAVKLRGFDGLIGVEIQPGRRLGTEMADYAK-KRGVSGIFHTDELPAYGITEEEVRGL 355
            + A+ L+GF G+IG E+QPGRRLGTE +D  K   GV G+FHTDELP YGITEEEV  L
Sbjct: 304 VIRAILLKGFSGMIGREVQPGRRLGTEFSDRGKVLGGVGGLFHTDELPKYGITEEEVTKL 363

Query: 356 RDAVGASQGDAVVMVAHERVTAENALREVIRRAEMAIQGVPEETRKALPDGNTQYLRPLP 415
           ++ +   + DAV++VA ++   E AL  VI RA+ ++ G+PEETRKAL DGNT YLRPLP
Sbjct: 364 KEYMNCGENDAVILVADKKNKVERALNAVIERAKESMIGIPEETRKALDDGNTSYLRPLP 423

Query: 416 TSSRMYLETDIPLFRIEDDLLEGIRRNLPELPSEKKERIMRDYGLSEDLASQLVKRNLVD 475
            ++RMY ETD+P   I ++ LE IR NLPE+P EK  R +++Y L+EDLA Q+V    VD
Sbjct: 424 GAARMYPETDVPTITITEEKLEAIRNNLPEMPEEKLVRFVKEYELNEDLAKQMVMSYHVD 483

Query: 476 EFEALTE--FRVDTTVIASLLAYTLRELRREGHDVDGLGLDELRDAIKLLEVGKISKDAL 533
            FE+L++   ++  T+IA+ L  TL+E++REG D D L  + L +  K L   K+SK+A+
Sbjct: 484 LFESLSKKYSKIKPTLIATTLEATLKEIKREGLDTDLLTEEHLEELFKGLSEDKMSKEAV 543

Query: 534 RDIVACMADEGLAAEDAARKLNLLL-------LAEDEIESIIQEIVEGNLDMISERGMGA 586
            D++          E+ ++KL+ +L       ++ DE+ESII++I+  N+  ++E+GMGA
Sbjct: 544 PDVIKGF------IENPSKKLDEILEIKGMSSMSVDEVESIIEDIINQNISQVNEKGMGA 597

Query: 587 MGPLMGQAMGRLRGRADGKVVNRILREKIQERL 619
           MG LMG+ M +LRG+ADGK++N  L++K++E++
Sbjct: 598 MGLLMGRCMAQLRGKADGKLINTTLQKKLKEKV 630


Lambda     K      H
   0.318    0.137    0.380 

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: 1084
Number of extensions: 48
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 619
Length of database: 631
Length adjustment: 37
Effective length of query: 582
Effective length of database: 594
Effective search space:   345708
Effective search space used:   345708
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: 54 (25.4 bits)

Align candidate WP_011868096.1 MMARC5_RS01665 (Glu-tRNA(Gln) amidotransferase subunit GatE)
to HMM TIGR00134 (gatE: glutamyl-tRNA(Gln) amidotransferase, subunit E (EC 6.3.5.-))

# 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/TIGR00134.hmm
# target sequence database:        /tmp/gapView.3935228.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00134  [M=622]
Accession:   TIGR00134
Description: gatE_arch: glutamyl-tRNA(Gln) amidotransferase, subunit E
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-295  967.4  20.2   1.6e-295  967.1  20.2    1.0  1  NCBI__GCF_000016125.1:WP_011868096.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016125.1:WP_011868096.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  967.1  20.2  1.6e-295  1.6e-295       3     621 ..       4     629 ..       2     630 .. 0.99

  Alignments for each domain:
  == domain 1  score: 967.1 bits;  conditional E-value: 1.6e-295
                             TIGR00134   3 dyekvGlkvGleihqqldtkrklfclcptllrdseedfeivrvlrpkrselGevdraaleeaerkkkfiykyy 75 
                                           dyek+GlkvGleihqql+tkrklfc+cpt +rd+e+++ei rvlrp++se+G+vd+aal e +++kkfiy+yy
  NCBI__GCF_000016125.1:WP_011868096.1   4 DYEKLGLKVGLEIHQQLNTKRKLFCNCPTKIRDDEPHGEIERVLRPSQSEMGHVDKAALLESKKEKKFIYQYY 76 
                                           9************************************************************************ PP

                             TIGR00134  76 ndttclveadeepprelneealeiavevalllnmevvdevhtmrkividGsntsGfqrtalvatdGyletdeg 148
                                           nd tclve+d+epp+++++ea+  a+ev+ l+nm++ dev +mrk+vidGsntsGfqrt++v+++G++et+ g
  NCBI__GCF_000016125.1:WP_011868096.1  77 NDSTCLVELDDEPPHDVSPEAVDTALEVSTLMNMKMADEVQIMRKMVIDGSNTSGFQRTMFVSQEGFIETEYG 149
                                           ************************************************************************* PP

                             TIGR00134 149 kvgieslcleedaarkiedrgdavvysldrlGiplveistepdikspkmakevaariGeilrstgkvkrGlGt 221
                                           ++g++slcleeda++kied++d+  y +drlGipl+ei+tepdi spkm ke+a+riG+ilr+tgkvkrGlGt
  NCBI__GCF_000016125.1:WP_011868096.1 150 NIGVTSLCLEEDACKKIEDGKDYTKYCVDRLGIPLLEITTEPDITSPKMGKEAARRIGTILRATGKVKRGLGT 222
                                           ************************************************************************* PP

                             TIGR00134 222 irqdvnisirdGarvevkGvqdldliekiverevlrqlnllkirdelkergaeveekifdvtevfkdtkskii 294
                                           irqdvnisir+Gar+evkGvq+ldlieki+e+ev rq++l +i++el +r+aev++ i d+te++kdt+sk++
  NCBI__GCF_000016125.1:WP_011868096.1 223 IRQDVNISIREGARIEVKGVQNLDLIEKIIENEVTRQISLNEIKEELLKRNAEVVDEIKDITELLKDTESKVL 295
                                           ************************************************************************* PP

                             TIGR00134 295 rnaek....vkavllrGfdGlvGkeiqpGrrlGteladiakki.GvgGvfhtdelpayGiteeevkklrdavg 362
                                           ++a+k    ++a+ll+Gf+G++G+e+qpGrrlGte++d+ k+  GvgG+fhtdelp+yGiteeev kl+++++
  NCBI__GCF_000016125.1:WP_011868096.1 296 KSALKnkgvIRAILLKGFSGMIGREVQPGRRLGTEFSDRGKVLgGVGGLFHTDELPKYGITEEEVTKLKEYMN 368
                                           **99999999*********************************99**************************** PP

                             TIGR00134 363 aeegdavvlvadeevkveralrevierakealvGvpeetrkaledGntaylrplpgaarmypetdippvvike 435
                                             e+dav+lvad++ kveral++vierake+++G+peetrkal+dGnt+ylrplpgaarmypetd+p + i+e
  NCBI__GCF_000016125.1:WP_011868096.1 369 CGENDAVILVADKKNKVERALNAVIERAKESMIGIPEETRKALDDGNTSYLRPLPGAARMYPETDVPTITITE 441
                                           ************************************************************************* PP

                             TIGR00134 436 elleeiranlpelpeekaerlkkeyklsedlakklvksnyvdvfeelskklk.vdptviasvleltlkelrre 507
                                           e le ir nlpe+peek  r+ key+l+edlak++v s++vd+fe lskk+  ++pt+ia++le tlke++re
  NCBI__GCF_000016125.1:WP_011868096.1 442 EKLEAIRNNLPEMPEEKLVRFVKEYELNEDLAKQMVMSYHVDLFESLSKKYSkIKPTLIATTLEATLKEIKRE 514
                                           **************************************************977******************** PP

                             TIGR00134 508 GvdidkleerelrevlklleeGkiakegleevlkllaeepdkaedearklk.lkllakeeiekiieeiieekl 579
                                           G d d l e++l+e +k l+e k++ke++ +v+k++ e+p k  de++++k +  ++ +e+e+iie+ii++++
  NCBI__GCF_000016125.1:WP_011868096.1 515 GLDTDLLTEEHLEELFKGLSEDKMSKEAVPDVIKGFIENPSKKLDEILEIKgMSSMSVDEVESIIEDIINQNI 587
                                           ***************************************************99999***************** PP

                             TIGR00134 580 dlikerGegafgplmGrvmkklrGkadGkvvneilrkklkea 621
                                             ++e+G+ga+g lmGr+m++lrGkadGk++n  l+kklke+
  NCBI__GCF_000016125.1:WP_011868096.1 588 SQVNEKGMGAMGLLMGRCMAQLRGKADGKLINTTLQKKLKEK 629
                                           ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (622 nodes)
Target sequences:                          1  (631 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 23.28
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis