Alignments for a candidate for gatA in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Burkholderia phytofirmans PsJN

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate BPHYT_RS01555 BPHYT_RS01555 glutamyl-tRNA(Gln) amidotransferase subunit A

Query= SwissProt::O06491
         (485 letters)



>FitnessBrowser__BFirm:BPHYT_RS01555
          Length = 495

 Score =  469 bits (1206), Expect = e-136
 Identities = 247/494 (50%), Positives = 337/494 (68%), Gaps = 15/494 (3%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           + +  +TEL+  +  KE    +L     KRI A +  + AF+ +D +   A AK  D A+
Sbjct: 1   MHEKSLTELRAALTAKECSAVELAQLYLKRIDAANS-LNAFIQVDPDLTLAQAKAAD-AL 58

Query: 63  DGRSEHGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKL 122
                 G L G+PI  KD  VTKG R+T  SK+L N++  +DATVV RLQ+A  V +GK 
Sbjct: 59  LHTGHAGPLVGLPIAHKDVFVTKGWRSTAGSKMLSNYESPFDATVVARLQNAGMVCVGKT 118

Query: 123 NMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQP 182
           NMDEFAMGSS ENS +   +NPW++  VPGGSSGGSAAAVAA   P + G+DTGGSIRQP
Sbjct: 119 NMDEFAMGSSNENSYFGPVQNPWDVKAVPGGSSGGSAAAVAARLAPAATGTDTGGSIRQP 178

Query: 183 ASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSAN 242
           ASF G+ G+KPTYGRVSRYG++AFASSLDQ GP+ ++  D A LL A++G D+ DSTS  
Sbjct: 179 ASFSGITGIKPTYGRVSRYGMIAFASSLDQGGPMAQSAADCATLLNAMAGFDERDSTSLV 238

Query: 243 VDVPDFL---------SSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGAT 293
            D  D+           S    + GL+I +PKEY G G+  + R SV AALK  E LGAT
Sbjct: 239 RDDEDYTRYLGKPWKEESAAKPLAGLRIGLPKEYFGAGLADDVRASVDAALKQYEALGAT 298

Query: 294 WEEVSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGN 353
             +VSLP ++ ++  YY+++ +EAS+NL+RFDG+R+G+R     +L+D+YK++RAEGFG 
Sbjct: 299 LVDVSLPKTELSIPVYYVIAPAEASSNLSRFDGVRFGHRAAEYRDLLDMYKKSRAEGFGP 358

Query: 354 EVKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGE 413
           EVKRRI++G + LS GYYDAYY +AQK+R +I +DF++ F++ DVI+GP  P+ A+ +G 
Sbjct: 359 EVKRRILVGAYVLSHGYYDAYYLQAQKIRRIIAQDFQEAFKQCDVIMGPVAPSVAWDLGA 418

Query: 414 NTKDPLTMYANDILTIPVNLAGVPGISVPCGLADGL----PLGLQIIGKHFDESTVYRVA 469
              DP+ MY  DI T+ V+LAG+PG+SVPCG   G     P+GLQIIG +F+E+ + +VA
Sbjct: 419 KGDDPVQMYLADIYTLSVSLAGLPGMSVPCGFGAGANAQRPVGLQIIGNYFNEARMLQVA 478

Query: 470 HAFEQATDHHKAKP 483
            AF++ATD H+  P
Sbjct: 479 DAFQRATDWHRKAP 492


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: 587
Number of extensions: 23
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: 495
Length adjustment: 34
Effective length of query: 451
Effective length of database: 461
Effective search space:   207911
Effective search space used:   207911
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 BPHYT_RS01555 BPHYT_RS01555 (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.18640.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
     6e-180  584.8   0.0   6.9e-180  584.7   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS01555  BPHYT_RS01555 glutamyl-tRNA(Gln)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS01555  BPHYT_RS01555 glutamyl-tRNA(Gln) amidotransferase subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  584.7   0.0  6.9e-180  6.9e-180       2     465 ..      10     486 ..       9     487 .. 0.96

  Alignments for each domain:
  == domain 1  score: 584.7 bits;  conditional E-value: 6.9e-180
                                TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 
                                              +++l++ke+s++e+++ +l+ri+a ++ +naf++v+++ +l++ak+ d+ ++  +  +l g+pia Kd++
  lcl|FitnessBrowser__BFirm:BPHYT_RS01555  10 RAALTAKECSAVELAQLYLKRIDAANS-LNAFIQVDPDLTLAQAKAADALLHtGHaGPLVGLPIAHKDVF 78 
                                              67899*********************9.*********************99865536************* PP

                                TIGR00132  70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpG 139
                                              ++k+++ t++Sk+L+ny sp+datVv rl++ag++ +GktN+DEFamGss e+S+fg+++nP++ + vpG
  lcl|FitnessBrowser__BFirm:BPHYT_RS01555  79 VTKGWRSTAGSKMLSNYESPFDATVVARLQNAGMVCVGKTNMDEFAMGSSNENSYFGPVQNPWDVKAVPG 148
                                              ********************************************************************** PP

                                TIGR00132 140 GSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkved 209
                                              GSsgGsaaavaa l+p a g+DTGgSiRqPAsf+g+ G+KPtYG+vSRyG++a+asSldq G++a++  d
  lcl|FitnessBrowser__BFirm:BPHYT_RS01555 149 GSSGGSAAAVAARLAPAATGTDTGGSIRQPASFSGITGIKPTYGRVSRYGMIAFASSLDQGGPMAQSAAD 218
                                              ********************************************************************** PP

                                TIGR00132 210 ialvldvisgkDkkDstslevkveelleelkk.........dlkglkvgvvkelseesldkevkekfekl 270
                                               a +l++++g D++Dstsl  ++e++++ l k          l gl++g+ ke+++ +l ++v+++++++
  lcl|FitnessBrowser__BFirm:BPHYT_RS01555 219 CATLLNAMAGFDERDSTSLVRDDEDYTRYLGKpwkeesaakPLAGLRIGLPKEYFGAGLADDVRASVDAA 288
                                              **********************999987654433334433356799************************ PP

                                TIGR00132 271 lekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfge 340
                                              l++ e+lga++v+vslp+ +l++++Yy+i+p+Eassnl+r+dg+r+G+r+ e+++l ++y+k+R+egfg 
  lcl|FitnessBrowser__BFirm:BPHYT_RS01555 289 LKQYEALGATLVDVSLPKTELSIPVYYVIAPAEASSNLSRFDGVRFGHRAAEYRDLLDMYKKSRAEGFGP 358
                                              ********************************************************************** PP

                                TIGR00132 341 evkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemyl 410
                                              evkrRi++Gay+ls++yyd+yy++Aqk+r++i+++f+++f+++Dvi++p+ap +a  lg+k +dp++myl
  lcl|FitnessBrowser__BFirm:BPHYT_RS01555 359 EVKRRILVGAYVLSHGYYDAYYLQAQKIRRIIAQDFQEAFKQCDVIMGPVAPSVAWDLGAKGDDPVQMYL 428
                                              ********************************************************************** PP

                                TIGR00132 411 sDvltvpanlaGlpaisvPlgkke...kglpiGlqiigkafddkkllsvakaleqald 465
                                              +D++t+ ++laGlp++svP+g       + p+Glqiig++f++ ++l+va a+++a+d
  lcl|FitnessBrowser__BFirm:BPHYT_RS01555 429 ADIYTLSVSLAGLPGMSVPCGFGAganAQRPVGLQIIGNYFNEARMLQVADAFQRATD 486
                                              ********************9753322789***********************99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (495 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: 00:00:00.03
# Mc/sec: 7.29
//
[ok]

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

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