Alignments for a candidate for gatA in Azohydromonas australica DSM 1124

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Azohydromonas australica DSM 1124

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_028996923.1 H537_RS0104390 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000430725.1:WP_028996923.1
          Length = 496

 Score =  449 bits (1156), Expect = e-131
 Identities = 238/489 (48%), Positives = 323/489 (66%), Gaps = 18/489 (3%)

Query: 8   ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67
           +  L + +  K+    +L      R+ A   ++ AF+ +D E A A A    +A D R  
Sbjct: 10  VAALSRALAAKDFSSVELTQHLLARV-ADHQQLGAFVHVDAEGALAAA----QAADARRA 64

Query: 68  HG---LLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNM 124
            G    L G+PI  KD  VT G  TT  SK+L+ +   +DATVV RL  A  V++GKLN 
Sbjct: 65  AGDATALTGVPIAHKDIFVTAGAPTTAGSKMLQGYQSPFDATVVARLAAAGVVSLGKLNC 124

Query: 125 DEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPAS 184
           DEFAMGS+ ENSA+    NPW+   VPGGSSGGSAAAVAA  +P + G+DTGGSIRQPAS
Sbjct: 125 DEFAMGSANENSAWGPALNPWDRTRVPGGSSGGSAAAVAARLLPAATGTDTGGSIRQPAS 184

Query: 185 FCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVD 244
           F G+ G+KPTYGR SRYG++AFASSLDQ GP+ R+ ED A LL A+SG D+ D+TSA   
Sbjct: 185 FSGITGIKPTYGRCSRYGMIAFASSLDQAGPMARSAEDCALLLSAMSGFDERDATSAERP 244

Query: 245 VPDFL---------SSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWE 295
             DF          +S    ++GL++ +P+E+  E +  +   +V  AL  LE LGAT  
Sbjct: 245 AEDFHAQMLQAREGASADKPLQGLRVGLPREFFPEALAADVNGAVRNALAELEKLGATLV 304

Query: 296 EVSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEV 355
           EVSLP ++ ++  YY+++ +EAS+NL R+DG+RYG R +   +L+D+YK+TRA+GFG EV
Sbjct: 305 EVSLPRTELSIPVYYIIAPAEASSNLQRYDGVRYGRRAEKYGDLVDMYKKTRAQGFGAEV 364

Query: 356 KRRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENT 415
           KRRIM+GT+ LS GYYDAYY +AQK+R +I  DF+  F+  DVI GP  P+ A+++G  +
Sbjct: 365 KRRIMIGTYVLSHGYYDAYYLQAQKLRRMIADDFQQCFQHCDVIAGPVAPSVAWQLGAKS 424

Query: 416 KDPLTMYANDILTIPVNLAGVPGISVPCGLAD-GLPLGLQIIGKHFDESTVYRVAHAFEQ 474
            DP+  Y  DI T+P +LAG+PG+SVP G  + G+P+GLQ+IG +F E  +   AHAF+Q
Sbjct: 425 DDPVAAYLADIFTLPASLAGLPGMSVPAGFGEGGMPVGLQLIGNYFAEGQLLHTAHAFQQ 484

Query: 475 ATDHHKAKP 483
           ATDHH   P
Sbjct: 485 ATDHHLRAP 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: 578
Number of extensions: 18
Number of successful extensions: 3
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_028996923.1 H537_RS0104390 (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.24878.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-175  570.9   0.0   1.2e-175  570.7   0.0    1.0  1  lcl|NCBI__GCF_000430725.1:WP_028996923.1  H537_RS0104390 Asp-tRNA(Asn)/Glu


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000430725.1:WP_028996923.1  H537_RS0104390 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 !  570.7   0.0  1.2e-175  1.2e-175       4     465 ..      16     487 ..      13     488 .. 0.96

  Alignments for each domain:
  == domain 1  score: 570.7 bits;  conditional E-value: 1.2e-175
                                 TIGR00132   4 llkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdnia 70 
                                               +l +k++s++e+++++l+r+  +++ + af++v++e al++a++ d++ a  + + l+g+pia Kd ++
  lcl|NCBI__GCF_000430725.1:WP_028996923.1  16 ALAAKDFSSVELTQHLLARVADHQQ-LGAFVHVDAEGALAAAQAADARRAaGDaTALTGVPIAHKDIFV 83 
                                               6788999***************999.********************998875547************** PP

                                 TIGR00132  71 vkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpG 139
                                               + + +tt++Sk+L++y+sp+datVv rl +ag++ +Gk N DEFamGs+ e+Sa+g+  nP++++rvpG
  lcl|NCBI__GCF_000430725.1:WP_028996923.1  84 TAGAPTTAGSKMLQGYQSPFDATVVARLAAAGVVSLGKLNCDEFAMGSANENSAWGPALNPWDRTRVPG 152
                                               ********************************************************************* PP

                                 TIGR00132 140 GSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkve 208
                                               GSsgGsaaavaa l p a g+DTGgSiRqPAsf+g+ G+KPtYG+ SRyG++a+asSldq G++a++ e
  lcl|NCBI__GCF_000430725.1:WP_028996923.1 153 GSSGGSAAAVAARLLPAATGTDTGGSIRQPASFSGITGIKPTYGRCSRYGMIAFASSLDQAGPMARSAE 221
                                               ********************************************************************* PP

                                 TIGR00132 209 dialvldvisgkDkkDstslevkveelleelkk.........dlkglkvgvvkelseesldkevkekfe 268
                                               d al+l+++sg D++D ts+e + e++  ++ +          l+gl+vg+ +e++ e l  +v+ +++
  lcl|NCBI__GCF_000430725.1:WP_028996923.1 222 DCALLLSAMSGFDERDATSAERPAEDFHAQMLQaregasadkPLQGLRVGLPREFFPEALAADVNGAVR 290
                                               **********************999886654332334555446899*********************** PP

                                 TIGR00132 269 kllekleelgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRseg 337
                                               ++l +le+lga++vevslp+ +l++++Yyii+p+Eassnl+rydg+ryG+r+e++ +l ++y+ktR++g
  lcl|NCBI__GCF_000430725.1:WP_028996923.1 291 NALAELEKLGATLVEVSLPRTELSIPVYYIIAPAEASSNLQRYDGVRYGRRAEKYGDLVDMYKKTRAQG 359
                                               ********************************************************************* PP

                                 TIGR00132 338 fgeevkrRimlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedpl 406
                                               fg+evkrRim+G+y+ls++yyd+yy++Aqk+r++i+d+f++ f+++Dvi++p+ap +a +lg+k +dp+
  lcl|NCBI__GCF_000430725.1:WP_028996923.1 360 FGAEVKRRIMIGTYVLSHGYYDAYYLQAQKLRRMIADDFQQCFQHCDVIAGPVAPSVAWQLGAKSDDPV 428
                                               ********************************************************************* PP

                                 TIGR00132 407 emylsDvltvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqald 465
                                               + yl+D++t+pa+laGlp++svP+g  e g+p+Glq+ig++f++ +ll+ a+a++qa+d
  lcl|NCBI__GCF_000430725.1:WP_028996923.1 429 AAYLADIFTLPASLAGLPGMSVPAGFGEGGMPVGLQLIGNYFAEGQLLHTAHAFQQATD 487
                                               *******************************************************9987 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.74
//
[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