Alignments for a candidate for gatB in Desulfarculus baarsii DSM 2075

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatB in Desulfarculus baarsii DSM 2075

Align Glutamyl-tRNA(Gln) amidotransferase subunit B, chloroplastic/mitochondrial; Glu-AdT subunit B; EC 6.3.5.- (characterized)
to candidate WP_013257673.1 DEBA_RS04255 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB

Query= SwissProt::Q9FV81
         (550 letters)



>NCBI__GCF_000143965.1:WP_013257673.1
          Length = 476

 Score =  476 bits (1226), Expect = e-139
 Identities = 237/479 (49%), Positives = 332/479 (69%), Gaps = 8/479 (1%)

Query: 69  DYEAVIGIETHVQLSTLTKAFCSCSNNYGSYPNTSICPVCMGLPGALPVLNSKVVEFGVR 128
           DYEAVIG+E H QL T +K FC CS ++G  PN+++CPVC+G+PG LPVLN +VVE  +R
Sbjct: 2   DYEAVIGLEVHAQLLTRSKIFCGCSTSFGQPPNSNVCPVCLGMPGVLPVLNQQVVELAMR 61

Query: 129 LGLALNCDLSLKSKFDRKQYFYPDLPKGYQISQFDIPIASGGYVDVDIPLEFGGGHRRFG 188
             LA  C ++ +S + RK YFYPDLPKGYQISQ+++P+A  G +++ +     G  +  G
Sbjct: 62  AALATGCQVAERSVWARKNYFYPDLPKGYQISQYELPLAQHGRLEITVD----GQEKCVG 117

Query: 189 ITRVHMEEDAGKLLHSDTGDYSQVDLNRAGVPLLEIVSEPDMRSGIEAAEYACEMQRIAR 248
           ITR+HMEEDAGKL+H  +   S VDLNR GVPL+EIVSEPDMRS  EA  Y   ++ I  
Sbjct: 118 ITRIHMEEDAGKLVHDPSLPQSYVDLNRTGVPLIEIVSEPDMRSPEEAGAYLRALRDILV 177

Query: 249 YLGVSNGNMQEGSLRCDVNISIRPIGQAEFGTKVEIKNLNAFSAISRAIDFEISRQALLY 308
           YL V +GNM+EGS RCD N+SIRP+GQ + GT+ E+KN+N+F  + +AID+EI RQ  + 
Sbjct: 178 YLEVCDGNMEEGSFRCDANVSIRPLGQEKLGTRAELKNMNSFRNVMKAIDYEIRRQKAIL 237

Query: 309 NQGKADQIVTETRLWEEGAQKTVTMRKKEGLADYRYFPEPDLPEVILTQEYVDSIRASLP 368
           ++G   Q++ +TRLW++ A KTV MR KE   DYRYFP+PDL  + +   ++  +   LP
Sbjct: 238 DEG--GQVIQQTRLWDDAAGKTVAMRGKEEAHDYRYFPDPDLLPLEIAPAWLARVGQGLP 295

Query: 369 ELPEAKRRRY-EAMGLGMQDVLFLANDVSVAEYFDAVIGKGAEVKLAANWIMSDIAAYLK 427
           ELP AKR+R+ +A GL   D   L  + ++A+YF+A +  GA  K AANWIMSD+   L+
Sbjct: 296 ELPAAKRQRFQQAHGLSAYDAEVLCAERALADYFEAAVNAGAPAKAAANWIMSDLLGALR 355

Query: 428 NEKLSINDIKLTPQELAELIAAIKDGTISGKIGKEILFELLAKGGTVKGMIKAKDLVQIT 487
            E  +I    +TPQ LAEL+A +  G ISGKI K+I   +L  G +   +++ K L Q++
Sbjct: 356 AEGQAIGQCAVTPQALAELLALVASGQISGKIAKDIFPLMLETGQSAATIVEQKGLRQVS 415

Query: 488 DPAEIEKMVIQVVSENPKQLEQYRSGKTKLQGYFAGQVMKMSKGKANPGLLNKILLEKL 546
           D  E++ ++ ++++E+PK+ E YR+GK KL GYF GQVMK +KG+ANP  +N+ L+EKL
Sbjct: 416 DSGELQAVLERIIAESPKEAEGYRAGKKKLMGYFVGQVMKATKGQANPQAVNE-LVEKL 473


Lambda     K      H
   0.317    0.134    0.379 

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: 708
Number of extensions: 32
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: 550
Length of database: 476
Length adjustment: 35
Effective length of query: 515
Effective length of database: 441
Effective search space:   227115
Effective search space used:   227115
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_013257673.1 DEBA_RS04255 (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.11500.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.1e-191  621.3   0.0   5.7e-191  621.1   0.0    1.0  1  lcl|NCBI__GCF_000143965.1:WP_013257673.1  DEBA_RS04255 Asp-tRNA(Asn)/Glu-t


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000143965.1:WP_013257673.1  DEBA_RS04255 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 !  621.1   0.0  5.7e-191  5.7e-191       2     480 ..       1     474 [.       1     475 [. 0.99

  Alignments for each domain:
  == domain 1  score: 621.1 bits;  conditional E-value: 5.7e-191
                                 TIGR00133   2 ieyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalns 70 
                                               ++ye+viGlEvH ql t+sK+Fc cs+++ + +pN+nvcpvclg+PG+lPvlN+++v+ A+  ala+++
  lcl|NCBI__GCF_000143965.1:WP_013257673.1   1 MDYEAVIGLEVHAQLLTRSKIFCGCSTSFGQ-PPNSNVCPVCLGMPGVLPVLNQQVVELAMRAALATGC 68 
                                               68****************************9.************************************* PP

                                 TIGR00133  71 kivsevsvFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleekekeigierlhlEeDtgksqykesd 139
                                               + v+e sv++RK+YfYpDlPkgyqi+q++lP+a++G+lei ++++ek +gi+r+h+EeD+gk+++  s 
  lcl|NCBI__GCF_000143965.1:WP_013257673.1  69 Q-VAERSVWARKNYFYPDLPKGYQISQYELPLAQHGRLEITVDGQEKCVGITRIHMEEDAGKLVHDPSL 136
                                               *.668*************************************************************886 PP

                                 TIGR00133 140 kdkqslvDfNRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkG 208
                                                  qs+vD+NR+gvPL+EiV++Pd++s++ea a+l+ lr il yle+ dg++eeGs+R+D+Nvsir+ G
  lcl|NCBI__GCF_000143965.1:WP_013257673.1 137 --PQSYVDLNRTGVPLIEIVSEPDMRSPEEAGAYLRALRDILVYLEVCDGNMEEGSFRCDANVSIRPLG 203
                                               ..7****************************************************************** PP

                                 TIGR00133 209 qekegtrvEiKNlnslksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYf 277
                                               qek gtr+E+KN+ns++++ kai+yEi Rqk++l +g +v q+tr +d++  +tv++R Kee++DYRYf
  lcl|NCBI__GCF_000143965.1:WP_013257673.1 204 QEKLGTRAELKNMNSFRNVMKAIDYEIRRQKAILDEGGQVIQQTRLWDDAAGKTVAMRGKEEAHDYRYF 272
                                               ********************************************************************* PP

                                 TIGR00133 278 pePdlppieideevvkekveeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepk 346
                                               p+Pdl p+ei++ ++ + v + lpelP akr+r+++  gls++da+vl +++ l+d+fe +v++ +++k
  lcl|NCBI__GCF_000143965.1:WP_013257673.1 273 PDPDLLPLEIAPAWLAR-VGQGLPELPAAKRQRFQQAHGLSAYDAEVLCAERALADYFEAAVNAGAPAK 340
                                               **************999.*************************************************** PP

                                 TIGR00133 347 lavnWileellgeLnkkkislaeallkpeelaeliklikegkisqksakelleellenkkdpkkliekl 415
                                               +a+nWi+++llg L+++   + +++++p++lael++l+  g+is+k+ak+++  +le+++++ +++e++
  lcl|NCBI__GCF_000143965.1:WP_013257673.1 341 AAANWIMSDLLGALRAEGQAIGQCAVTPQALAELLALVASGQISGKIAKDIFPLMLETGQSAATIVEQK 409
                                               ********************************************************************* PP

                                 TIGR00133 416 gliqisdekelvkiveevikenpkevekyksgkekalkflvGqvmkktkgradpkevekllkell 480
                                               gl q+sd  el++++e +i+e pke e y++gk+k+++++vGqvmk tkg+a+p+ v++l+++ll
  lcl|NCBI__GCF_000143965.1:WP_013257673.1 410 GLRQVSDSGELQAVLERIIAESPKEAEGYRAGKKKLMGYFVGQVMKATKGQANPQAVNELVEKLL 474
                                               **************************************************************988 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.70
//
[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