Alignments for a candidate for gatA in Burkholderia vietnamiensis G4

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Burkholderia vietnamiensis G4

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_011886344.1 glutamyl-tRNA(Gln) amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000016205.1:WP_011886344.1
          Length = 496

 Score =  477 bits (1227), Expect = e-139
 Identities = 252/490 (51%), Positives = 334/490 (68%), Gaps = 16/490 (3%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           +TEL+  +  KE    +L     KRI A  D + AF+ +D +   A AK  D  +  R  
Sbjct: 6   LTELRAALAAKECSAVELAQLYLKRIDAARD-LNAFVHVDADLTLAQAKAADAEL-ARGA 63

Query: 68  HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127
            G L G+PI  KD  VT+G R+T  SK+LEN+   +DATVV RLQ A  VT+GK NMDEF
Sbjct: 64  GGPLTGVPIAHKDVFVTRGWRSTAGSKMLENYQSPFDATVVARLQAAGMVTLGKTNMDEF 123

Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187
           AMGSS ENSA+   KNPW+   VPGGSSGGS+AAVAA   P + G+DTGGSIRQPASF G
Sbjct: 124 AMGSSNENSAFGAVKNPWDTHAVPGGSSGGSSAAVAARLAPAATGTDTGGSIRQPASFAG 183

Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247
           V G+KPTYGRVSRYG++AFASSLDQ GP+ ++  D A LL A++G D+ DSTS   D  D
Sbjct: 184 VTGIKPTYGRVSRYGMIAFASSLDQGGPMAQSASDCALLLNAMAGFDERDSTSLERDDED 243

Query: 248 FL----------SSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEV 297
           F           S     + GL+I +P EY G G+  + R ++ AALK  E LGAT   V
Sbjct: 244 FTRHLGQPWTAGSDAARPLAGLRIGLPNEYFGAGLADDVRATIDAALKQYEALGATLVPV 303

Query: 298 SLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKR 357
           SLP ++ ++  YY+++ +EAS+NL+RFDG+R+G+R     +L+D+YK++RAEGFG EVKR
Sbjct: 304 SLPKTELSIPVYYVIAPAEASSNLSRFDGVRFGHRAAQYGDLLDMYKKSRAEGFGPEVKR 363

Query: 358 RIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKD 417
           RI++GT+ LS GYYDAYY +AQK+R +I +DF++ F+  DVI+GP +PT A+ +G    D
Sbjct: 364 RILVGTYVLSHGYYDAYYLQAQKIRRIIAQDFQEAFKSCDVIMGPASPTVAWDLGAKGDD 423

Query: 418 PLTMYANDILTIPVNLAGVPGISVPCGLADGL----PLGLQIIGKHFDESTVYRVAHAFE 473
           P+ MY  DI T+ V+LAG+PG+SVPCG   G     P+GLQIIG +F+E+ + +VA AF+
Sbjct: 424 PVQMYLADIYTLSVSLAGLPGMSVPCGFGAGANAKRPVGLQIIGNYFNEARMLQVADAFQ 483

Query: 474 QATDHHKAKP 483
           +ATD HK  P
Sbjct: 484 RATDWHKQVP 493


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: 602
Number of extensions: 25
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: 496
Length adjustment: 34
Effective length of query: 451
Effective length of database: 462
Effective search space:   208362
Effective search space used:   208362
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 WP_011886344.1 (glutamyl-tRNA(Gln) amidotransferase subunit A)
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.1648863.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-179  583.5   0.0   1.8e-179  583.3   0.0    1.0  1  NCBI__GCF_000016205.1:WP_011886344.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016205.1:WP_011886344.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  583.3   0.0  1.8e-179  1.8e-179       2     465 ..      10     487 ..       9     488 .. 0.96

  Alignments for each domain:
  == domain 1  score: 583.3 bits;  conditional E-value: 1.8e-179
                             TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdniavk 72 
                                           +++l +ke+s++e+++ +l+ri+a +d +naf++v+++ +l++ak+ d+++a     +l+g+pia Kd+++++
  NCBI__GCF_000016205.1:WP_011886344.1  10 RAALAAKECSAVELAQLYLKRIDAARD-LNAFVHVDADLTLAQAKAADAELArGAgGPLTGVPIAHKDVFVTR 81 
                                           678999********************9.***********************964545**************** PP

                             TIGR00132  73 diettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGGSsgGs 145
                                           +++ t++Sk+Leny+sp+datVv rl++ag++++GktN+DEFamGss e+Safg++knP++++ vpGGSsgGs
  NCBI__GCF_000016205.1:WP_011886344.1  82 GWRSTAGSKMLENYQSPFDATVVARLQAAGMVTLGKTNMDEFAMGSSNENSAFGAVKNPWDTHAVPGGSSGGS 154
                                           ************************************************************************* PP

                             TIGR00132 146 aaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkvedialvldvis 218
                                           +aavaa l+p a g+DTGgSiRqPAsf+gv G+KPtYG+vSRyG++a+asSldq G++a++ +d al+l++++
  NCBI__GCF_000016205.1:WP_011886344.1 155 SAAVAARLAPAATGTDTGGSIRQPASFAGVTGIKPTYGRVSRYGMIAFASSLDQGGPMAQSASDCALLLNAMA 227
                                           ************************************************************************* PP

                             TIGR00132 219 gkDkkDstslevkveelleelkk..........dlkglkvgvvkelseesldkevkekfekllekleelgaei 281
                                           g D++Dstsle ++e+++++l +           l gl++g+ +e+++ +l ++v+++++++l++ e+lga++
  NCBI__GCF_000016205.1:WP_011886344.1 228 GFDERDSTSLERDDEDFTRHLGQpwtagsdaarPLAGLRIGLPNEYFGAGLADDVRATIDAALKQYEALGATL 300
                                           *****************998876666666544457799*********************************** PP

                             TIGR00132 282 vevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRimlGayals 354
                                           v+vslp+ +l++++Yy+i+p+Eassnl+r+dg+r+G+r+ ++ +l ++y+k+R+egfg evkrRi++G+y+ls
  NCBI__GCF_000016205.1:WP_011886344.1 301 VPVSLPKTELSIPVYYVIAPAEASSNLSRFDGVRFGHRAAQYGDLLDMYKKSRAEGFGPEVKRRILVGTYVLS 373
                                           ************************************************************************* PP

                             TIGR00132 355 keyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltvpanlaGlpais 427
                                           ++yyd+yy++Aqk+r++i+++f+++f+++Dvi++p++pt+a  lg+k +dp++myl+D++t+ ++laGlp++s
  NCBI__GCF_000016205.1:WP_011886344.1 374 HGYYDAYYLQAQKIRRIIAQDFQEAFKSCDVIMGPASPTVAWDLGAKGDDPVQMYLADIYTLSVSLAGLPGMS 446
                                           ************************************************************************* PP

                             TIGR00132 428 vPlgkke...kglpiGlqiigkafddkkllsvakaleqald 465
                                           vP+g         p+Glqiig++f++ ++l+va a+++a+d
  NCBI__GCF_000016205.1:WP_011886344.1 447 VPCGFGAganAKRPVGLQIIGNYFNEARMLQVADAFQRATD 487
                                           ***9753222789***********************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (496 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 29.34
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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