Alignments for a candidate for gatB in Nitratiruptor tergarcus DSM 16512

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Nitratiruptor tergarcus DSM 16512

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate WP_084275993.1 B8779_RS07835 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9RF06
         (475 letters)



>NCBI__GCF_900176045.1:WP_084275993.1
          Length = 476

 Score =  441 bits (1135), Expect = e-128
 Identities = 229/476 (48%), Positives = 317/476 (66%), Gaps = 5/476 (1%)

Query: 1   MHFETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAM 60
           M FE VIGLEVHV+L T +KMF   P  F    N NT  + LA PG LPV+N+ AV  AM
Sbjct: 1   MEFEVVIGLEVHVQLNTKTKMFCSCPTSFAQRQNKNTCPVCLALPGALPVINEEAVKKAM 60

Query: 61  RAAMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEV-DGETKRIGIT 119
               A++  I  +S F+RKNYFYPD PK YQISQF+ PI E GY+ I+  DG  ++IGIT
Sbjct: 61  MFGWAIDATINKKSIFNRKNYFYPDLPKGYQISQFEIPIVERGYLFIDKEDGSKRKIGIT 120

Query: 120 RLHMEEDAGKSTHKGEYSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           R H+EEDAGK+ H+GE S VDLNR GTPL+EIVS+PDIRS +EA  YL+KL +I++Y  +
Sbjct: 121 RAHLEEDAGKNIHEGEISKVDLNRAGTPLLEIVSDPDIRSSEEAVQYLKKLHAIVRYLDI 180

Query: 180 SDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSG- 238
           SD  M+EGS RCDAN+S+RP G EK  T+ E+KNLNSF ++++ ++YE +R  E    G 
Sbjct: 181 SDANMQEGSFRCDANVSIRPKGDEKLYTRVEIKNLNSFRFIQRAIDYEVQRHIEAWEDGV 240

Query: 239 --GEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELP 296
              E+ QETR FD + G T  MR KE S DYRYFP+PD++PL I + + E+ +  IPELP
Sbjct: 241 YDEEVVQETRLFDTNKGVTRSMRGKEESADYRYFPDPDLLPLVIPEEFFEKTK-NIPELP 299

Query: 297 DERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQ 356
           D+++ +++ E G+  YDA +L  +KE + FFE  +  G + K    WL   +   LN+  
Sbjct: 300 DQKRDRFIQEYGIKPYDAALLAESKERAHFFEEMVATGIEPKNAVTWLTVELAARLNEKG 359

Query: 357 VELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGLVQISDEA 416
           +++  + +  + LA +++ IED T+S K AK V   L  +  +  + +E  GL QI+D  
Sbjct: 360 LDITSSPVDSQKLAKLVQRIEDKTISGKAAKDVLDYLMEESVDVDEAIEKLGLKQITDTG 419

Query: 417 TLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQEL 472
            +   ++E L  NE+ V +YK GK K  GF VGQ+MKASKG+A+P+LVN+LL+++L
Sbjct: 420 AIETMIDEILAKNEEKVAEYKAGKEKLFGFFVGQVMKASKGKADPKLVNELLRKKL 475


Lambda     K      H
   0.313    0.133    0.373 

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: 655
Number of extensions: 24
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: 475
Length of database: 476
Length adjustment: 33
Effective length of query: 442
Effective length of database: 443
Effective search space:   195806
Effective search space used:   195806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate WP_084275993.1 B8779_RS07835 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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/TIGR00133.hmm
# target sequence database:        /tmp/gapView.8256.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00133  [M=481]
Accession:   TIGR00133
Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-193  628.2   1.2   4.4e-193  628.1   1.2    1.0  1  lcl|NCBI__GCF_900176045.1:WP_084275993.1  B8779_RS07835 Asp-tRNA(Asn)/Glu-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900176045.1:WP_084275993.1  B8779_RS07835 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  628.1   1.2  4.4e-193  4.4e-193       2     480 ..       1     475 [.       1     476 [] 0.98

  Alignments for each domain:
  == domain 1  score: 628.1 bits;  conditional E-value: 4.4e-193
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               +e+e+viGlEvHvqlntk+K+Fc+c++++ +  +N+n+cpvcl+lPGalPv+N+eavkkA++ + a+++
  lcl|NCBI__GCF_900176045.1:WP_084275993.1   1 MEFEVVIGLEVHVQLNTKTKMFCSCPTSFAQ-RQNKNTCPVCLALPGALPVINEEAVKKAMMFGWAIDA 68 
                                               689***************************9.9************************************ PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke.keigierlhlEeDtgksqykes 138
                                                i+ ++s+F+RK+YfYpDlPkgyqi+q+++Pi+e G+l i++e+++ ++igi+r hlEeD+gk+ ++++
  lcl|NCBI__GCF_900176045.1:WP_084275993.1  69 TIN-KKSIFNRKNYFYPDLPKGYQISQFEIPIVERGYLFIDKEDGSkRKIGITRAHLEEDAGKNIHEGE 136
                                               *66.69***********************************99876379******************66 PP

                                 TIGR00133 139 dkdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlk 207
                                                   +s vD+NR+g+PLlEiV+ Pd++s++ea+++lkkl++i+ryl+isd++++eGs+R+D+Nvsir+k
  lcl|NCBI__GCF_900176045.1:WP_084275993.1 137 ----ISKVDLNRAGTPLLEIVSDPDIRSSEEAVQYLKKLHAIVRYLDISDANMQEGSFRCDANVSIRPK 201
                                               ....79*************************************************************** PP

                                 TIGR00133 208 GqekegtrvEiKNlnslksiekaieyEieRqkkllkkg...eevkqetrafdekksitvslRkKeeseD 273
                                               G+ek +trvEiKNlns++ i++ai+yE++R ++++++g   eev+qetr fd++k +t s+R Kees+D
  lcl|NCBI__GCF_900176045.1:WP_084275993.1 202 GDEKLYTRVEIKNLNSFRFIQRAIDYEVQRHIEAWEDGvydEEVVQETRLFDTNKGVTRSMRGKEESAD 270
                                               ********************************************************************* PP

                                 TIGR00133 274 YRYfpePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvkli 342
                                               YRYfp+Pdl p++i ee+ ++  ++++pelP++kr r+ +eyg++ +da +l + +e ++ fee+v + 
  lcl|NCBI__GCF_900176045.1:WP_084275993.1 271 YRYFPDPDLLPLVIPEEFFEK--TKNIPELPDQKRDRFIQEYGIKPYDAALLAESKERAHFFEEMVATG 337
                                               *****************9988..899******************************************* PP

                                 TIGR00133 343 kepklavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkl 411
                                                epk+av+W++ el+++Ln+k ++++ + +++++la+l++ i++++is+k+ak++l+ l+e+  d+++ 
  lcl|NCBI__GCF_900176045.1:WP_084275993.1 338 IEPKNAVTWLTVELAARLNEKGLDITSSPVDSQKLAKLVQRIEDKTISGKAAKDVLDYLMEESVDVDEA 406
                                               ********************************************************************* PP

                                 TIGR00133 412 ieklgliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               ieklgl qi+d+ ++  +++e++++n+++v +yk+gkek+++f+vGqvmk +kg+adpk v++ll+++l
  lcl|NCBI__GCF_900176045.1:WP_084275993.1 407 IEKLGLKQITDTGAIETMIDEILAKNEEKVAEYKAGKEKLFGFFVGQVMKASKGKADPKLVNELLRKKL 475
                                               ******************************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (476 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 6.79
//
[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