Alignments for a candidate for gatA in Denitrovibrio acetiphilus DSM 12809

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Denitrovibrio acetiphilus DSM 12809

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_013011689.1 DACET_RS12225 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA

Query= SwissProt::O06491
         (485 letters)



>NCBI__GCF_000025725.1:WP_013011689.1
          Length = 486

 Score =  504 bits (1297), Expect = e-147
 Identities = 255/482 (52%), Positives = 341/482 (70%), Gaps = 11/482 (2%)

Query: 1   MSLFDHKITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDE 60
           MS  +  + EL   +  K+    +LV     RI+  D ++QAF  ++E      A +  E
Sbjct: 1   MSFLNKNLKELTDGLAGKDFSSKELVQFYLDRIKKYDSEIQAFNYINEN-----ALKQAE 55

Query: 61  AVDGRSEHGLLF----GMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEA 116
           A+D +   G       G+P+ +KD ++TK + TTCSSK LE F P ++ T V  L++A  
Sbjct: 56  AIDAKRLKGETLPAYAGVPVALKDLLITKDMPTTCSSKFLEGFKPPFNGTAVSLLEEAGF 115

Query: 117 VTIGKLNMDEFAMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTG 176
           + +GKL+MDEFAMGSS EN+A+K T+NPW+   VPGGSSGGSAA+VAAG  P +LGSDTG
Sbjct: 116 INLGKLSMDEFAMGSSNENAAFKKTRNPWDTTKVPGGSSGGSAASVAAGLAPVTLGSDTG 175

Query: 177 GSIRQPASFCGVVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKM 236
           GSIRQPAS CGVVG+KPTYGRVSR+GLVAFASSLDQIGP+ ++  D A +L  I   D  
Sbjct: 176 GSIRQPASLCGVVGMKPTYGRVSRFGLVAFASSLDQIGPMGKSAFDLASILSVIGKHDSK 235

Query: 237 DSTSANVDVPDFLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEE 296
           DSTSANVD  D+   LT D++G+KI +PKEY  EG+  + + +V  A+K    LG    +
Sbjct: 236 DSTSANVDQKDYTKDLTDDVRGMKIGIPKEYFAEGLAPDVKSAVADAIKKYTDLGCEMVD 295

Query: 297 VSLPHSKYALATYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVK 356
           +SLPH+ YALATYY+++++EAS+NL R+DG+R+G R + ADNL D+Y  +R EGFG EVK
Sbjct: 296 ISLPHTDYALATYYIIATAEASSNLGRYDGVRFGRRAE-ADNLRDMYFNSRTEGFGEEVK 354

Query: 357 RRIMLGTFALSSGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTK 416
           RRIMLGT+ LS+GYYDAYY KAQ+VRTLIK+DF + F+  D I+ PT+PT AFK G  T+
Sbjct: 355 RRIMLGTYVLSAGYYDAYYLKAQRVRTLIKQDFVEAFKTVDAIICPTSPTTAFKAGAKTE 414

Query: 417 DPLTMYANDILTIPVNLAGVPGISVPCGL-ADGLPLGLQIIGKHFDESTVYRVAHAFEQA 475
           DPL MY +DI T+ +NL G  G+S+PCG   DG+P+G+Q++G +F+E  +  +AHAFE A
Sbjct: 415 DPLQMYLSDIYTLSLNLFGGCGLSLPCGFDKDGMPIGVQLMGNYFEEGKILNLAHAFELA 474

Query: 476 TD 477
           TD
Sbjct: 475 TD 476


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: 654
Number of extensions: 28
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: 486
Length adjustment: 34
Effective length of query: 451
Effective length of database: 452
Effective search space:   203852
Effective search space used:   203852
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_013011689.1 DACET_RS12225 (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.32387.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-185  603.3   0.0   1.7e-185  603.1   0.0    1.0  1  lcl|NCBI__GCF_000025725.1:WP_013011689.1  DACET_RS12225 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025725.1:WP_013011689.1  DACET_RS12225 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 !  603.1   0.0  1.7e-185  1.7e-185       6     464 ..      16     475 ..      11     477 .. 0.97

  Alignments for each domain:
  == domain 1  score: 603.1 bits;  conditional E-value: 1.7e-185
                                 TIGR00132   6 kkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke..kklagipiavKdniav 71 
                                                 k++s+ke+++ +l+ri++ +++i+af  +++ +alk+a+++d+k    e     ag+p+a+Kd + +
  lcl|NCBI__GCF_000025725.1:WP_013011689.1  16 AGKDFSSKELVQFYLDRIKKYDSEIQAFNYINE-NALKQAEAIDAKRLkGEtlPAYAGVPVALKDLLIT 83 
                                               6688999********************977765.5********99766444234889************ PP

                                 TIGR00132  72 kdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervpGG 140
                                               kd++ttc+Sk+Le++++p++ t v +l+eag + +Gk  +DEFamGss e+ af+ t+nP+++++vpGG
  lcl|NCBI__GCF_000025725.1:WP_013011689.1  84 KDMPTTCSSKFLEGFKPPFNGTAVSLLEEAGFINLGKLSMDEFAMGSSNENAAFKKTRNPWDTTKVPGG 152
                                               ********************************************************************* PP

                                 TIGR00132 141 SsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkved 209
                                               SsgGsaa+vaa+l+p++lgsDTGgSiRqPAs+cgvvG+KPtYG+vSR+Glva+asSldqiG++ k+  d
  lcl|NCBI__GCF_000025725.1:WP_013011689.1 153 SSGGSAASVAAGLAPVTLGSDTGGSIRQPASLCGVVGMKPTYGRVSRFGLVAFASSLDQIGPMGKSAFD 221
                                               ********************************************************************* PP

                                 TIGR00132 210 ialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfekllekleelg 278
                                               +a +l+vi ++D+kDsts++v++++++++l++d++g+k+g+ ke++ e+l  +vk++++++++k ++lg
  lcl|NCBI__GCF_000025725.1:WP_013011689.1 222 LASILSVIGKHDSKDSTSANVDQKDYTKDLTDDVRGMKIGIPKEYFAEGLAPDVKSAVADAIKKYTDLG 290
                                               ********************************************************************* PP

                                 TIGR00132 279 aeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrRim 347
                                               +e+v++slp+ ++ala+Yyii+++Eassnl rydg+r+G+r+e ++ l+++y+++R egfgeevkrRim
  lcl|NCBI__GCF_000025725.1:WP_013011689.1 291 CEMVDISLPHTDYALATYYIIATAEASSNLGRYDGVRFGRRAEADN-LRDMYFNSRTEGFGEEVKRRIM 358
                                               ******************************************9998.********************** PP

                                 TIGR00132 348 lGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvltv 416
                                               lG+y+ls++yyd+yy+kAq+vrtli+++f ++f+ vD i++pt+pt+afk g+k+edpl+mylsD++t+
  lcl|NCBI__GCF_000025725.1:WP_013011689.1 359 LGTYVLSAGYYDAYYLKAQRVRTLIKQDFVEAFKTVDAIICPTSPTTAFKAGAKTEDPLQMYLSDIYTL 427
                                               ********************************************************************* PP

                                 TIGR00132 417 panlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464
                                                +nl G +++s+P+g +++g+piG+q++g++f++ k+l++a+a+e a+
  lcl|NCBI__GCF_000025725.1:WP_013011689.1 428 SLNLFGGCGLSLPCGFDKDGMPIGVQLMGNYFEEGKILNLAHAFELAT 475
                                               *******************************************99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (466 nodes)
Target sequences:                          1  (486 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: 7.80
//
[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