Alignments for a candidate for gatA in Acidovorax sp. GW101-3H11

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Acidovorax sp. GW101-3H11

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate Ac3H11_3338 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3338
          Length = 497

 Score =  459 bits (1182), Expect = e-134
 Identities = 237/493 (48%), Positives = 329/493 (66%), Gaps = 12/493 (2%)

Query: 2   SLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEA 61
           +L D  + +L   + ++ +   +       R QA    + A++A++ E   A A+  D A
Sbjct: 5   ALHDLGVAQLATELRERRVSAVEAAQHFLDRAQA-HQNLGAYVAVNPEITLAQARAQDAA 63

Query: 62  VDGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGK 121
           +   +  G L G+PI  KD  VTKG  +T  SK+L  +   +DATVV +L DA AVT+GK
Sbjct: 64  IAAGTA-GPLAGVPIAHKDIFVTKGFPSTAGSKMLAGYQSPFDATVVTKLADAGAVTLGK 122

Query: 122 LNMDEFAMGSSTENSAYKLT--------KNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGS 173
           LN DEFAMGS+ ENSA            +NPW  D +PGGSSGGSA AVAA   P   G+
Sbjct: 123 LNCDEFAMGSANENSAVAPVGTDAPAPVRNPWATDRIPGGSSGGSAVAVAARLAPAVTGT 182

Query: 174 DTGGSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGV 233
           DTGGSIRQPASFCG+ G+KPTYGR SRYG++AFASSLDQ GP+ R+ ED A LL A+ G 
Sbjct: 183 DTGGSIRQPASFCGITGIKPTYGRASRYGMIAFASSLDQAGPMARSAEDCALLLSAMCGP 242

Query: 234 DK-MDSTSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGA 292
           D   DSTS +V   +F + L   I+GL+I +P E+ GEG+  + R +V  ALK  E LGA
Sbjct: 243 DPDRDSTSLDVPAENFSAKLNDSIEGLRIGIPAEFFGEGLAPDVRAAVDGALKEYEKLGA 302

Query: 293 TWEEVSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFG 352
               +SLP ++ ++  YY+++ +EAS+NL+RFDG+++G+R  +  +L+D+YK+TRAEGFG
Sbjct: 303 KLVPISLPRTQLSIPVYYIIAPAEASSNLSRFDGVKFGHRAKDYSDLVDMYKKTRAEGFG 362

Query: 353 NEVKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIG 412
           +EVKRRIM+G + LS GYYDAYY +AQK+R +I  DF++ F+  D+I GP  PT A+K+G
Sbjct: 363 DEVKRRIMIGAYVLSHGYYDAYYLQAQKIRRMIADDFQNAFKSCDLIAGPVAPTVAWKLG 422

Query: 413 ENTKDPLTMYANDILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHA 471
           ++  DPL  Y  DI T+P +LAG+PG+SVP G  + G+P+GLQ++G +F E+ +   AH 
Sbjct: 423 DHGNDPLADYLADIFTLPGSLAGLPGMSVPAGFGEGGMPVGLQLLGNYFQEARLLNAAHR 482

Query: 472 FEQATDHHKAKPE 484
            +QATD H  +PE
Sbjct: 483 LQQATDFHLRRPE 495


Lambda     K      H
   0.315    0.134    0.381 

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: 632
Number of extensions: 26
Number of successful extensions: 4
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: 485
Length of database: 497
Length adjustment: 34
Effective length of query: 451
Effective length of database: 463
Effective search space:   208813
Effective search space used:   208813
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate Ac3H11_3338 (Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7))
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit (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/TIGR00132.hmm
# target sequence database:        /tmp/gapView.13881.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00132  [M=466]
Accession:   TIGR00132
Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   1.2e-172  560.8   0.0   1.4e-172  560.6   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3338  Aspartyl-tRNA(Asn) amidotransfer


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3338  Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamy
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  560.6   0.0  1.4e-172  1.4e-172       4     465 ..      17     488 ..      14     489 .. 0.97

  Alignments for each domain:
  == domain 1  score: 560.6 bits;  conditional E-value: 1.4e-172
                                        TIGR00132   4 llkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipi 63 
                                                       l +++vs++e+++++l+r +a+++ + a+++v++e +l++a++ d+++a  +  +lag+pi
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3338  17 ELRERRVSAVEAAQHFLDRAQAHQN-LGAYVAVNPEITLAQARAQDAAIAaGTaGPLAGVPI 77 
                                                      678899******************9.***********************975536******* PP

                                        TIGR00132  64 avKdniavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSaf 125
                                                      a Kd +++k+++ t++Sk+L +y+sp+datVv++l +aga+++Gk N DEFamGs+ e+Sa 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3338  78 AHKDIFVTKGFPSTAGSKMLAGYQSPFDATVVTKLADAGAVTLGKLNCDEFAMGSANENSAV 139
                                                      ************************************************************98 PP

                                        TIGR00132 126 g........vtknPeneervpGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlK 179
                                                               +++nP++++r+pGGSsgGsa avaa l+p   g+DTGgSiRqPAsfcg+ G+K
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3338 140 ApvgtdapaPVRNPWATDRIPGGSSGGSAVAVAARLAPAVTGTDTGGSIRQPASFCGITGIK 201
                                                      622222222579************************************************** PP

                                        TIGR00132 180 PtYGlvSRyGlvayasSldqiGilakkvedialvldvisgkD.kkDstslevkveelleelk 240
                                                      PtYG+ SRyG++a+asSldq G++a++ ed al+l++++g D  +Dstsl+v+ e++  +l+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3338 202 PTYGRASRYGMIAFASSLDQAGPMARSAEDCALLLSAMCGPDpDRDSTSLDVPAENFSAKLN 263
                                                      ******************************************559***************** PP

                                        TIGR00132 241 kdlkglkvgvvkelseesldkevkekfekllekleelgaeivevslpsvklalaiYyiisps 302
                                                      + + gl++g+  e+++e+l  +v+++++ +l++ e+lga++v++slp+ +l++++Yyii+p+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3338 264 DSIEGLRIGIPAEFFGEGLAPDVRAAVDGALKEYEKLGAKLVPISLPRTQLSIPVYYIIAPA 325
                                                      ************************************************************** PP

                                        TIGR00132 303 EassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayalskeyydkyykk 364
                                                      Eassnl+r+dg+++G+r++++++l ++y+ktR+egfg+evkrRim+Gay+ls++yyd+yy++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3338 326 EASSNLSRFDGVKFGHRAKDYSDLVDMYKKTRAEGFGDEVKRRIMIGAYVLSHGYYDAYYLQ 387
                                                      ************************************************************** PP

                                        TIGR00132 365 AqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpai 426
                                                      Aqk+r++i+d+f+++f+++D+i++p+apt+a klg++ +dpl+ yl+D++t+p +laGlp++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3338 388 AQKIRRMIADDFQNAFKSCDLIAGPVAPTVAWKLGDHGNDPLADYLADIFTLPGSLAGLPGM 449
                                                      ************************************************************** PP

                                        TIGR00132 427 svPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                                      svP+g  e g+p+Glq+ g++f++ +ll++a+ l+qa+d
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3338 450 SVPAGFGEGGMPVGLQLLGNYFQEARLLNAAHRLQQATD 488
                                                      **********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (497 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: 10.41
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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