Alignments for a candidate for gatA in Paraburkholderia sp. CCGE1002

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Paraburkholderia sp. CCGE1002

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_013088064.1 BC1002_RS00235 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000092885.1:WP_013088064.1
          Length = 495

 Score =  473 bits (1217), Expect = e-138
 Identities = 250/494 (50%), Positives = 338/494 (68%), Gaps = 15/494 (3%)

Query: 3   LFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAV 62
           + +  +TEL+  +  KE    +L     KRI A +  + AF+ +D E   A AK  D A+
Sbjct: 1   MHEKSLTELRAALAAKECSAVELAQLYLKRIDAANS-LNAFIQVDPELTLAQAKAAD-AL 58

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

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

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

Query: 243 VDVPDFLSSLTGD---------IKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGAT 293
            +  D+   L            + GL+I +PKEY G G+  E R S+ AALK  E LGAT
Sbjct: 239 HEPEDYTRYLGKSWRDGGAEKPLAGLRIGLPKEYFGAGLADEVRASIDAALKQYEALGAT 298

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

Query: 354 EVKRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGE 413
           EVKRRI++GT+ LS GYYDAYY +AQK+R +I +DF++ F++ DVI+GP  P+ A+ IG 
Sbjct: 359 EVKRRILVGTYVLSHGYYDAYYLQAQKIRRIIAQDFQEAFKQCDVIMGPVAPSVAWDIGA 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 DAFQRATDWHRQAP 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: 565
Number of extensions: 16
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 WP_013088064.1 BC1002_RS00235 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
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.19562.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-181  588.3   0.0     6e-181  588.1   0.0    1.0  1  lcl|NCBI__GCF_000092885.1:WP_013088064.1  BC1002_RS00235 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013088064.1  BC1002_RS00235 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  588.1   0.0    6e-181    6e-181       2     465 ..      10     486 ..       9     487 .. 0.96

  Alignments for each domain:
  == domain 1  score: 588.1 bits;  conditional E-value: 6e-181
                                 TIGR00132   2 kellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdn 68 
                                               +++l +ke+s++e+++ +l+ri+a ++ +naf++v++e +l++ak+ d+ ++  +  +l g+pia Kd+
  lcl|NCBI__GCF_000092885.1:WP_013088064.1  10 RAALAAKECSAVELAQLYLKRIDAANS-LNAFIQVDPELTLAQAKAADALLHtGHaGPLVGLPIAHKDV 77 
                                               678999********************9.*********************99865536************ PP

                                 TIGR00132  69 iavkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneerv 137
                                               +++k+++ t++Sk+L ny sp+datVv rl++ag++ +GktN+DEFamGss e+S+fg+++nP++++ v
  lcl|NCBI__GCF_000092885.1:WP_013088064.1  78 FVTKGWRSTAGSKMLANYESPFDATVVARLQNAGMVCVGKTNMDEFAMGSSNENSYFGAVQNPWDRKAV 146
                                               ********************************************************************* PP

                                 TIGR00132 138 pGGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakk 206
                                               pGGSsgGsaaavaa l+p a g+DTGgSiRqPAsf+g+ G+KPtYG+vSRyG++a+asSldq G++a++
  lcl|NCBI__GCF_000092885.1:WP_013088064.1 147 PGGSSGGSAAAVAARLAPAATGTDTGGSIRQPASFSGITGIKPTYGRVSRYGMIAFASSLDQGGPMAQS 215
                                               ********************************************************************* PP

                                 TIGR00132 207 vedialvldvisgkDkkDstslevkveelleelkk.........dlkglkvgvvkelseesldkevkek 266
                                                 d a +l++++g D++Dstsl+ ++e++++ l k          l gl++g+ ke+++ +l +ev+++
  lcl|NCBI__GCF_000092885.1:WP_013088064.1 216 AADCATLLNAMAGFDERDSTSLSHEPEDYTRYLGKswrdggaekPLAGLRIGLPKEYFGAGLADEVRAS 284
                                               ***************************9998776545445543356799******************** PP

                                 TIGR00132 267 fekllekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRs 335
                                               ++++l++ e+lga++vevslp+ +l++++Yy+i+p+Eassnl+r+dg+r+G+r+ e+++l ++y+k+R+
  lcl|NCBI__GCF_000092885.1:WP_013088064.1 285 IDAALKQYEALGATLVEVSLPKTELSIPVYYVIAPAEASSNLSRFDGVRFGHRAAEYRDLLDMYKKSRA 353
                                               ********************************************************************* PP

                                 TIGR00132 336 egfgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaed 404
                                               egfg evkrRi++G+y+ls++yyd+yy++Aqk+r++i+++f+++f+++Dvi++p+ap +a  +g+k +d
  lcl|NCBI__GCF_000092885.1:WP_013088064.1 354 EGFGPEVKRRILVGTYVLSHGYYDAYYLQAQKIRRIIAQDFQEAFKQCDVIMGPVAPSVAWDIGAKGDD 422
                                               ********************************************************************* PP

                                 TIGR00132 405 plemylsDvltvpanlaGlpaisvPlgkke...kglpiGlqiigkafddkkllsvakaleqald 465
                                               p++myl+D++t+ ++laGlp++svP+g       + p+Glqiig++f++ ++l+va a+++a+d
  lcl|NCBI__GCF_000092885.1:WP_013088064.1 423 PVQMYLADIYTLSVSLAGLPGMSVPCGFGAganAQRPVGLQIIGNYFNEARMLQVADAFQRATD 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: 00:00:00.01
# Mc/sec: 11.93
//
[ok]

This GapMind analysis is from Apr 10 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