Alignments for a candidate for gatE in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatE in Archaeoglobus veneficus SNP6

Align glutamyl-tRNA(Gln) amidotransferase subunit E (EC 6.3.5.7) (characterized)
to candidate WP_232215828.1 ARCVE_RS04520 Glu-tRNA(Gln) amidotransferase subunit GatE

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



>NCBI__GCF_000194625.1:WP_232215828.1
          Length = 626

 Score =  574 bits (1480), Expect = e-168
 Identities = 318/620 (51%), Positives = 416/620 (67%), Gaps = 10/620 (1%)

Query: 2   DWEKVGLKMGLEIHQQLDTESKLFCPCRTELTD-SEPDHDIVRNLRPTQSELGKFDRAAF 60
           D+E +GLK+G+EIHQQLDT+ KLFC C T   D  E + +  R LR  +SE+G+ DRAA 
Sbjct: 12  DYEALGLKVGIEIHQQLDTKHKLFCYCPTIQRDVEESNFEFFRYLRSKRSEMGEVDRAAK 71

Query: 61  EEAMRKLHFHYENYHEETCLVEADEEPPHPLNPEALEIAVTIALLLNMRVVDEFHTMRKQ 120
           EE  R   F Y+ Y + TCLVEADEEPP  LN EAL++A+ IA +LNM VVDE H MRK 
Sbjct: 72  EEVARSKKFIYKAY-DTTCLVEADEEPPRELNREALQVAILIARMLNMEVVDEVHVMRKI 130

Query: 121 VIDGSNTGGFQRTGLVATDGHLETPQGTVKIENLCLEEDAARRIRETGDGVVFRLDRLGI 180
           VIDGSNT GFQRT L+A DG++E     + +  LCLEE+A R++ + G  VV+ LDRLGI
Sbjct: 131 VIDGSNTTGFQRTALIAFDGYIECEGKKIGVATLCLEEEACRKVEDRGSEVVYSLDRLGI 190

Query: 181 PLVEITTDPSMSDPQQLREVAYQIGQILRST-RVKRGLGTIRQDLNISIRDGARVEVKGV 239
           PLVEI T P ++ P++ +EVA ++G ILRST RVKRGLGTIRQD+NISIRDGARVE+KGV
Sbjct: 191 PLVEIGTMPDITSPKEAKEVAAKLGMILRSTGRVKRGLGTIRQDVNISIRDGARVEIKGV 250

Query: 240 QDLDLIPEIVEREVKRQLSLVEIRDTLQERGAVVEDKIFDVSEVFADTESRIISSAESVL 299
           Q LD++ +IVE EV RQL+L++IRD L  RGA V ++IFDV+ +F++T+S++I  A+ V 
Sbjct: 251 QTLDILDKIVEYEVLRQLNLLKIRDELLARGASVVNQIFDVTSIFSNTKSKVIKRAKCVK 310

Query: 300 AVKLRGFDGLIGVEIQPGRRLGTEMADYAKKRGVSGIFHTDELPAYGITEEEVRGLRDAV 359
           A+ L+GF GL+G EIQPGRRLGTE AD AK  G+ GIFHTDELPAYGI+EEEV  LR  V
Sbjct: 311 AILLKGFAGLVGKEIQPGRRLGTEFADIAKTFGLGGIFHTDELPAYGISEEEVAELRRFV 370

Query: 360 GASQGDAVVMVAHERVTAENALREVIRRAEMAIQGVPEETRKALPDGNTQYLRPLPTSSR 419
           GA   DAV++ A E    ENAL  +I RAE  + GVPEETRKA  DG T YLRPLP ++R
Sbjct: 371 GAESNDAVILAAGEATRVENALARIIERAEYCLIGVPEETRKANEDGTTSYLRPLPGAAR 430

Query: 420 MYLETDIPLFRIEDDLLEGIRRNLPELPSEKKERIMRDYGLSEDLASQLVKRNLVDEFEA 479
           MY ETD+P  RI  D+LE     +PEL  E+ +R    YGL  DLA  +    L   FE 
Sbjct: 431 MYPETDVPAVRITPDMLE---VEIPELIEERAKRYAETYGLPYDLAYVMADSALHHLFEE 487

Query: 480 LTEFRVDTTVIASLLAYTLRELRREGHDVDGLGLDELRDAIKLLEVGKISKDALRDIVAC 539
             E ++  T +A +L     EL++EG ++  L     R  ++L+E GKI+K+   + +  
Sbjct: 488 FAE-KLPATTVARVLHIAPAELKKEGVEIGKLEEGHFRAVLELIEEGKIAKEGAEEALKI 546

Query: 540 MADEGLAAEDAARKLNLLLLAEDEIESIIQEIVEGNLDMISERGMGAMGPLMGQAMGRLR 599
             ++  A ++   ++   + +   ++S I +++E   D I ERG  A  PLMG  M   R
Sbjct: 547 FCEKPTATKE---EVVSSIGSATNLDSFIAKLMEEKKDFIKERGASAFKPLMGLVMKEFR 603

Query: 600 GRADGKVVNRILREKIQERL 619
           G+ DGKVV   L E I+  L
Sbjct: 604 GKVDGKVVAEKLNEAIKRAL 623


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: 1019
Number of extensions: 56
Number of successful extensions: 7
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: 619
Length of database: 626
Length adjustment: 37
Effective length of query: 582
Effective length of database: 589
Effective search space:   342798
Effective search space used:   342798
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_232215828.1 ARCVE_RS04520 (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.3063530.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1014.5  14.6          0 1014.3  14.6    1.0  1  NCBI__GCF_000194625.1:WP_232215828.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000194625.1:WP_232215828.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1014.3  14.6         0         0       3     622 .]      12     623 ..      10     623 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1014.3 bits;  conditional E-value: 0
                             TIGR00134   3 dyekvGlkvGleihqqldtkrklfclcptllrdsee.dfeivrvlrpkrselGevdraaleeaerkkkfiyky 74 
                                           dye +GlkvG+eihqqldtk+klfc cpt+ rd+ee +fe++r+lr krse+Gevdraa+ee+ r+kkfiyk 
  NCBI__GCF_000194625.1:WP_232215828.1  12 DYEALGLKVGIEIHQQLDTKHKLFCYCPTIQRDVEEsNFEFFRYLRSKRSEMGEVDRAAKEEVARSKKFIYKA 84 
                                           9*********************************999************************************ PP

                             TIGR00134  75 yndttclveadeepprelneealeiavevalllnmevvdevhtmrkividGsntsGfqrtalvatdGyletde 147
                                           y dttclveadeeppreln+eal++a+ +a++lnmevvdevh+mrkividGsnt+Gfqrtal+a+dGy+e ++
  NCBI__GCF_000194625.1:WP_232215828.1  85 Y-DTTCLVEADEEPPRELNREALQVAILIARMLNMEVVDEVHVMRKIVIDGSNTTGFQRTALIAFDGYIECEG 156
                                           *.*********************************************************************** PP

                             TIGR00134 148 gkvgieslcleedaarkiedrgdavvysldrlGiplveistepdikspkmakevaariGeilrstgkvkrGlG 220
                                           +k+g+++lclee+a+rk+edrg  vvysldrlGiplvei+t pdi spk akevaa++G+ilrstg+vkrGlG
  NCBI__GCF_000194625.1:WP_232215828.1 157 KKIGVATLCLEEEACRKVEDRGSEVVYSLDRLGIPLVEIGTMPDITSPKEAKEVAAKLGMILRSTGRVKRGLG 229
                                           ************************************************************************* PP

                             TIGR00134 221 tirqdvnisirdGarvevkGvqdldliekiverevlrqlnllkirdelkergaeveekifdvtevfkdtkski 293
                                           tirqdvnisirdGarve+kGvq ld+++kive+evlrqlnllkirdel  rga v+++ifdvt +f++tksk+
  NCBI__GCF_000194625.1:WP_232215828.1 230 TIRQDVNISIRDGARVEIKGVQTLDILDKIVEYEVLRQLNLLKIRDELLARGASVVNQIFDVTSIFSNTKSKV 302
                                           ************************************************************************* PP

                             TIGR00134 294 irnaekvkavllrGfdGlvGkeiqpGrrlGteladiakkiGvgGvfhtdelpayGiteeevkklrdavgaeeg 366
                                           i+ a+ vka+ll+Gf+GlvGkeiqpGrrlGte+adiak+ G+gG+fhtdelpayGi+eeev +lr +vgae +
  NCBI__GCF_000194625.1:WP_232215828.1 303 IKRAKCVKAILLKGFAGLVGKEIQPGRRLGTEFADIAKTFGLGGIFHTDELPAYGISEEEVAELRRFVGAESN 375
                                           ************************************************************************* PP

                             TIGR00134 367 davvlvadeevkveralrevierakealvGvpeetrkaledGntaylrplpgaarmypetdippvvikeelle 439
                                           dav+l+a+e+++ve+al ++iera+ +l+Gvpeetrka+edG+t+ylrplpgaarmypetd+p v+i+ ++le
  NCBI__GCF_000194625.1:WP_232215828.1 376 DAVILAAGEATRVENALARIIERAEYCLIGVPEETRKANEDGTTSYLRPLPGAARMYPETDVPAVRITPDMLE 448
                                           ************************************************************************* PP

                             TIGR00134 440 eiranlpelpeekaerlkkeyklsedlakklvksnyvdvfeelskklkvdptviasvleltlkelrreGvdid 512
                                              +++pel+ee+a+r+ + y+l+ dla  +++s + ++fee+++kl   +t +a+vl+++++el++eGv+i 
  NCBI__GCF_000194625.1:WP_232215828.1 449 ---VEIPELIEERAKRYAETYGLPYDLAYVMADSALHHLFEEFAEKLP--ATTVARVLHIAPAELKKEGVEIG 516
                                           ...******************************************999..999******************** PP

                             TIGR00134 513 kleerelrevlklleeGkiakegleevlkllaeepdkaedearklklkllakeeiekiieeiieekldliker 585
                                           klee ++r vl+l+eeGkiakeg+ee+lk+++e+p ++++   ++   ++++ +++++i++++eek d+iker
  NCBI__GCF_000194625.1:WP_232215828.1 517 KLEEGHFRAVLELIEEGKIAKEGAEEALKIFCEKPTATKE---EVVSSIGSATNLDSFIAKLMEEKKDFIKER 586
                                           ***********************************66655...566799************************ PP

                             TIGR00134 586 GegafgplmGrvmkklrGkadGkvvneilrkklkeal 622
                                           G  af+plmG+vmk++rGk+dGkvv+e+l++++k al
  NCBI__GCF_000194625.1:WP_232215828.1 587 GASAFKPLMGLVMKEFRGKVDGKVVAEKLNEAIKRAL 623
                                           *********************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (622 nodes)
Target sequences:                          1  (626 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: 00:00:00.01
# Mc/sec: 20.58
//
[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